5UMK | pdb_00005umk

Crystal structure of H62Y mutant of human macrophage migration inhibitory factor

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
C	d5umkc_	Alpha and beta proteins (a+b)	Tautomerase/MIF	Tautomerase/MIF	MIF-related	Microphage migration inhibition factor (MIF)	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d5umkb_	Alpha and beta proteins (a+b)	Tautomerase/MIF	Tautomerase/MIF	MIF-related	Microphage migration inhibition factor (MIF)	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d5umka_	Alpha and beta proteins (a+b)	Tautomerase/MIF	Tautomerase/MIF	MIF-related	Microphage migration inhibition factor (MIF)	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
C	SCOP2B Superfamily	Tautomerase/MIF	8036060	3001770	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Tautomerase/MIF	8036060	3001770	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Tautomerase/MIF	8036060	3001770	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
C	SAM_KSR1_N	e5umkC1	A: alpha bundles	X: Periplasmic binding protein-like II	H: Rubredoxin-related	T: Tetrapyrrole methylase C-terminal domain	F: SAM_KSR1_N	ECOD (develop294)
B	SAM_KSR1_N	e5umkB1	A: alpha bundles	X: Periplasmic binding protein-like II	H: Rubredoxin-related	T: Tetrapyrrole methylase C-terminal domain	F: SAM_KSR1_N	ECOD (develop294)
A	SAM_KSR1_N	e5umkA1	A: alpha bundles	X: Periplasmic binding protein-like II	H: Rubredoxin-related	T: Tetrapyrrole methylase C-terminal domain	F: SAM_KSR1_N	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
C	3.30.429.10	Alpha Beta	2-Layer Sandwich	Macrophage Migration Inhibitory Factor	Macrophage Migration Inhibitory Factor	CATH (4.3.0)
B	3.30.429.10	Alpha Beta	2-Layer Sandwich	Macrophage Migration Inhibitory Factor	Macrophage Migration Inhibitory Factor	CATH (4.3.0)
A	3.30.429.10	Alpha Beta	2-Layer Sandwich	Macrophage Migration Inhibitory Factor	Macrophage Migration Inhibitory Factor	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C	PF01187	Macrophage migration inhibitory factor (MIF) (MIF)	Macrophage migration inhibitory factor (MIF)		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C	Macrophage migration inhibitory factor	intramolecular oxidoreductase activity, interconverting keto- and enol-groups isomerase activity intramolecular oxidoreductase activity phenylpyruvate tautomerase activity catalytic activity protein binding binding signaling receptor binding cytokine receptor binding intramolecular oxidoreductase activity, transposing C=C bonds dopachrome isomerase activity identical protein binding enzyme binding protease binding intramolecular oxidoreductase activity, interconverting keto- and enol-groups isomerase activity intramolecular oxidoreductase activity phenylpyruvate tautomerase activity catalytic activity protein binding binding signaling receptor binding cytokine receptor binding intramolecular oxidoreductase activity, transposing C=C bonds dopachrome isomerase activity identical protein binding enzyme binding protease binding molecular function activator activity molecular function regulator activity cytokine activity signaling receptor regulator activity receptor ligand activity signaling receptor activator activity chemoattractant activity	cellular response to stimulus negative regulation of mononuclear cell migration negative regulation of locomotion regulation of cell motility regulation of cellular process response to stimulus negative regulation of biological process negative regulation of chemotaxis macrophage migration taxis negative regulation of macrophage chemotaxis cell migration regulation of immune system process regulation of mononuclear cell migration cellular response to stimulus negative regulation of mononuclear cell migration negative regulation of locomotion regulation of cell motility regulation of cellular process response to stimulus negative regulation of biological process negative regulation of chemotaxis macrophage migration taxis negative regulation of macrophage chemotaxis cell migration regulation of immune system process regulation of mononuclear cell migration negative regulation of macrophage migration negative regulation of cell migration chemotaxis regulation of biological process regulation of leukocyte chemotaxis regulation of leukocyte migration response to external stimulus leukocyte migration negative regulation of leukocyte migration regulation of response to stimulus regulation of locomotion response to chemical negative regulation of response to external stimulus negative regulation of cell motility negative regulation of leukocyte chemotaxis regulation of response to external stimulus macrophage chemotaxis regulation of macrophage migration negative regulation of cellular process regulation of cell migration myeloid leukocyte migration cell motility locomotion cell chemotaxis regulation of macrophage chemotaxis negative regulation of response to stimulus biological regulation regulation of chemotaxis cellular response to chemical stimulus negative regulation of immune system process immune system process mononuclear cell migration cellular process leukocyte chemotaxis multicellular organismal process regulation of B cell apoptotic process homeostatic process leukocyte apoptotic process regulation of programmed cell death lymphocyte apoptotic process negative regulation of leukocyte apoptotic process negative regulation of mature B cell apoptotic process regulation of leukocyte apoptotic process regulation of lymphocyte apoptotic process mature B cell apoptotic process negative regulation of programmed cell death regulation of apoptotic process B cell apoptotic process cell death negative regulation of B cell apoptotic process B cell homeostasis negative regulation of apoptotic process multicellular organismal-level homeostasis leukocyte homeostasis homeostasis of number of cells regulation of mature B cell apoptotic process lymphocyte homeostasis apoptotic process programmed cell death negative regulation of lymphocyte apoptotic process biological process involved in interspecies interaction between organisms immune response response to other organism defense response defense response to symbiont response to biotic stimulus defense response to other organism response to stress innate immune response response to external biotic stimulus regulation of localization positive regulation of arachidonate secretion transport positive regulation of biological process regulation of lipid transport regulation of arachidonate secretion localization arachidonate secretion monocarboxylic acid transport positive regulation of secretion fatty acid transport icosanoid transport regulation of icosanoid secretion icosanoid secretion long-chain fatty acid transport positive regulation of icosanoid secretion organic anion transport carboxylic acid transport secretion arachidonate transport regulation of transport lipid localization lipid transport positive regulation of lipid localization establishment of localization regulation of fatty acid transport regulation of secretion positive regulation of organic acid transport organic acid transport positive regulation of lipid transport positive regulation of transport regulation of lipid localization macromolecule localization regulation of organic acid transport positive regulation of fatty acid transport cellular response to stress cellular senescence regulation of immune effector process positive regulation of macromolecule biosynthetic process positive regulation of metabolic process positive regulation of biosynthetic process positive regulation of myeloid leukocyte cytokine production involved in immune response cytokine production regulation of cytokine production positive regulation of immune effector process positive regulation of macromolecule metabolic process regulation of multicellular organismal process myeloid leukocyte cytokine production cytokine production involved in immune response positive regulation of immune system process positive regulation of cellular process production of molecular mediator of immune response regulation of biosynthetic process regulation of cytokine production involved in immune response regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process immune effector process regulation of gene expression biosynthetic process positive regulation of gene expression positive regulation of cytokine production involved in immune response positive regulation of production of molecular mediator of immune response positive regulation of multicellular organismal process metabolic process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of production of molecular mediator of immune response positive regulation of cytokine production regulation of metabolic process regulation of macrophage activation regulation of leukocyte activation cell activation regulation of cell activation myeloid leukocyte activation leukocyte activation macrophage activation chemokine (C-X-C motif) ligand 2 production regulation of chemokine (C-X-C motif) ligand 2 production positive regulation of chemokine (C-X-C motif) ligand 2 production regulation of chemokine production chemokine production positive regulation of chemokine production regulation of protein metabolic process negative regulation of metabolic process primary metabolic process regulation of primary metabolic process protein metabolic process negative regulation of protein metabolic process negative regulation of macromolecule metabolic process positive regulation of cell communication regulation of lipopolysaccharide-mediated signaling pathway positive regulation of response to biotic stimulus regulation of response to biotic stimulus positive regulation of signal transduction response to lipid signaling cellular response to lipopolysaccharide regulation of signal transduction cell communication positive regulation of response to stimulus lipopolysaccharide-mediated signaling pathway cellular response to biotic stimulus positive regulation of response to external stimulus response to bacterium signal transduction regulation of signaling cell surface receptor signaling pathway response to oxygen-containing compound cellular response to molecule of bacterial origin response to lipopolysaccharide cellular response to oxygen-containing compound cellular response to lipid regulation of cell communication positive regulation of lipopolysaccharide-mediated signaling pathway response to molecule of bacterial origin positive regulation of signaling positive regulation of cell population proliferation positive regulation of B cell proliferation lymphocyte activation leukocyte proliferation positive regulation of lymphocyte activation positive regulation of cell activation regulation of B cell proliferation lymphocyte proliferation regulation of B cell activation positive regulation of leukocyte activation positive regulation of mononuclear cell proliferation regulation of lymphocyte proliferation regulation of leukocyte proliferation cell population proliferation B cell activation positive regulation of lymphocyte proliferation B cell proliferation positive regulation of B cell activation regulation of cell population proliferation mononuclear cell proliferation positive regulation of leukocyte proliferation regulation of mononuclear cell proliferation regulation of lymphocyte activation protein-containing complex organization protein trimerization cellular component organization cellular component biogenesis cellular component assembly protein homotrimerization protein complex oligomerization protein-containing complex assembly protein homooligomerization cellular component organization or biogenesis intracellular signal transduction positive regulation of ERK1 and ERK2 cascade regulation of intracellular signal transduction intracellular signaling cassette positive regulation of MAPK cascade positive regulation of intracellular signal transduction regulation of MAPK cascade MAPK cascade ERK1 and ERK2 cascade regulation of ERK1 and ERK2 cascade fibroblast proliferation regulation of fibroblast proliferation positive regulation of fibroblast proliferation icosanoid metabolic process prostaglandin metabolic process unsaturated fatty acid metabolic process oxoacid metabolic process lipid biosynthetic process organic acid biosynthetic process organic acid metabolic process carboxylic acid biosynthetic process prostanoid metabolic process icosanoid biosynthetic process small molecule metabolic process prostaglandin biosynthetic process prostanoid biosynthetic process fatty acid metabolic process monocarboxylic acid biosynthetic process small molecule biosynthetic process carboxylic acid metabolic process fatty acid biosynthetic process unsaturated fatty acid biosynthetic process monocarboxylic acid metabolic process lipid metabolic process negative regulation of signaling negative regulation of intracellular signal transduction regulation of cellular response to stress DNA damage response, signal transduction by p53 class mediator negative regulation of cell communication regulation of response to stress regulation of signal transduction by p53 class mediator negative regulation of DNA damage response, signal transduction by p53 class mediator regulation of DNA damage response, signal transduction by p53 class mediator negative regulation of signal transduction by p53 class mediator signal transduction by p53 class mediator negative regulation of signal transduction DNA damage response signal transduction in response to DNA damage regulation of intrinsic apoptotic signaling pathway in response to DNA damage regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator negative regulation of apoptotic signaling pathway negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator intrinsic apoptotic signaling pathway in response to DNA damage intrinsic apoptotic signaling pathway negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage intrinsic apoptotic signaling pathway by p53 class mediator regulation of apoptotic signaling pathway regulation of intrinsic apoptotic signaling pathway intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator apoptotic signaling pathway negative regulation of intrinsic apoptotic signaling pathway negative regulation of intrinsic apoptotic signaling pathway by p53 class mediator regulation of intrinsic apoptotic signaling pathway by p53 class mediator myeloid cell apoptotic process negative regulation of myeloid cell apoptotic process regulation of myeloid cell apoptotic process regulation of cellular senescence negative regulation of cellular senescence positive regulation of phosphorylation positive regulation of phosphorus metabolic process phosphorylation positive regulation of phosphate metabolic process phosphate-containing compound metabolic process regulation of phosphorus metabolic process regulation of phosphorylation phosphorus metabolic process inflammatory response negative regulation of gene expression negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process positive regulation of cAMP/PKA signal transduction cAMP/PKA signal transduction regulation of cAMP/PKA signal transduction regulation of tumor necrosis factor production positive regulation of tumor necrosis factor superfamily cytokine production tumor necrosis factor superfamily cytokine production positive regulation of tumor necrosis factor production tumor necrosis factor production regulation of tumor necrosis factor superfamily cytokine production	extracellular exosome membrane-bounded organelle extracellular vesicle cellular anatomical structure extracellular organelle extracellular region organelle extracellular space vesicle extracellular membrane-bounded organelle intracellular anatomical structure cytoplasm cytosol cell surface extracellular exosome membrane-bounded organelle extracellular vesicle cellular anatomical structure extracellular organelle extracellular region organelle extracellular space vesicle extracellular membrane-bounded organelle intracellular anatomical structure cytoplasm cytosol cell surface cell periphery plasma membrane membrane membrane-enclosed lumen intracellular vesicle ficolin-1-rich granule intracellular membrane-bounded organelle endomembrane system intracellular organelle lumen intracellular organelle organelle lumen cytoplasmic vesicle ficolin-1-rich granule lumen secretory granule secretory vesicle nucleus nucleoplasm nuclear lumen vesicle lumen cytoplasmic vesicle lumen secretory granule lumen

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C	IPR001398	Macrophage migration inhibitory factor	Family
A, B, C	IPR019829	Macrophage migration inhibitory factor, conserved site	Conserved Site
A, B, C	IPR014347	Tautomerase/MIF superfamily	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B, C	Pharos: P14174	juvenile idiopathic arthritis rheumatoid arthritis Stevens-Johnson syndrome endogenous depression malignant mesothelioma prostate cancer carcinoma melancholia Memory Disorders keloid breast carcinoma sarcomatoid carcinoma colitis toxic epidermal necrolysis schizophrenia juvenile idiopathic arthritis rheumatoid arthritis Stevens-Johnson syndrome endogenous depression malignant mesothelioma prostate cancer carcinoma melancholia Memory Disorders keloid breast carcinoma sarcomatoid carcinoma colitis toxic epidermal necrolysis schizophrenia dilated cardiomyopathy undifferentiated carcinoma mammary neoplasms, animal alopecia areata anxiety disorder breast cancer depressive disorder systemic-onset juvenile idiopathic arthritis neurotic disorder autism

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.