8VR5 | pdb_00008vr5

crystal structure of the Pcryo_0618 aminotransferase from Psychrobacter cryohalolentis K5 in the presence of PMP and glutamate

PDB DOI: https://doi.org/10.2210/pdb8VR5/pdb

Classification: TRANSFERASE
Organism(s): Psychrobacter cryohalolentis K5
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2024-01-20 Released: 2024-01-31
Deposition Author(s): Bockhaus, N.J., Thoden, J.B., Holden, H.M.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free:
0.213 (Depositor), 0.220 (DCC)
R-Value Work:
0.178 (Depositor), 0.180 (DCC)
R-Value Observed:
0.180 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Biochemical Investigation of the Enzymes Required for the Production of 2,3,4-triacetoamido-2,3,4-trideoxy-l-arabinose in Psychrobacter cryohalolentis K5

Bockhaus, N.J., Dunsirn, M.M., Thoden, J.B., Holden, H.M.

To be published.

Macromolecule Content

Total Structure Weight: 171.42 kDa
Atom Count: 12,658
Modeled Residue Count: 1,497
Deposited Residue Count: 1,520
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DegT/DnrJ/EryC1/StrS aminotransferase	A, B, C, D	380	Psychrobacter cryohalolentis K5	Mutation(s): 0 Gene Names: Pcryo_0618
UniProt
Find proteins for Q1QD52 (Psychrobacter cryohalolentis (strain ATCC BAA-1226 / DSM 17306 / VKM B-2378 / K5)) Explore Q1QD52 Go to UniProtKB: Q1QD52
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q1QD52
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PDG (Subject of Investigation/LOI) Query on PDG Download Ideal Coordinates CCD File SDF format, chain M [auth B] SDF format, chain V [auth C] SDF format, chain Y [auth D] MOL2 format, chain M [auth B] MOL2 format, chain V [auth C] MOL2 format, chain Y [auth D] mmCIF format, chain M [auth B] mmCIF format, chain V [auth C] mmCIF format, chain Y [auth D]	M [auth B], V [auth C], Y [auth D]	N-({3-HYDROXY-2-METHYL-5-[(PHOSPHONOOXY)METHYL]PYRIDIN-4-YL}METHYL)-D-GLUTAMIC ACID C₁₃ H₁₉ N₂ O₉ P JMRKOGDJNHPMHS-SNVBAGLBSA-N		Interactions Focus chain M [auth B] Focus chain V [auth C] Focus chain Y [auth D] Interactions & Density Focus chain M [auth B] Focus chain V [auth C] Focus chain Y [auth D]
A1ADI Query on A1ADI Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain N [auth B] SDF format, chain O [auth B] MOL2 format, chain F [auth A] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] mmCIF format, chain F [auth A] mmCIF format, chain N [auth B] mmCIF format, chain O [auth B]	F [auth A], N [auth B], O [auth B]	2,2'-(1,4-diazepane-1,4-diyl)di(ethane-1-sulfonic acid) C₉ H₂₀ N₂ O₆ S₂ QZTMPPUJIVQNKS-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain N [auth B] Focus chain O [auth B] Interactions & Density Focus chain F [auth A] Focus chain N [auth B] Focus chain O [auth B]
PMP (Subject of Investigation/LOI) Query on PMP Download Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE C₈ H₁₃ N₂ O₅ P ZMJGSOSNSPKHNH-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain Q [auth B] SDF format, chain R [auth B] SDF format, chain S [auth B] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth B] MOL2 format, chain S [auth B] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain Q [auth B] mmCIF format, chain R [auth B] mmCIF format, chain S [auth B]	H [auth A] I [auth A] J [auth A] K [auth A] Q [auth B] H [auth A], I [auth A], J [auth A], K [auth A], Q [auth B], R [auth B], S [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Interactions & Density Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain P [auth B] SDF format, chain W [auth C] MOL2 format, chain G [auth A] MOL2 format, chain P [auth B] MOL2 format, chain W [auth C] mmCIF format, chain G [auth A] mmCIF format, chain P [auth B] mmCIF format, chain W [auth C]	G [auth A], P [auth B], W [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain G [auth A] Focus chain P [auth B] Focus chain W [auth C] Interactions & Density Focus chain G [auth A] Focus chain P [auth B] Focus chain W [auth C]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain L [auth A] SDF format, chain T [auth B] SDF format, chain Z [auth D] MOL2 format, chain L [auth A] MOL2 format, chain T [auth B] MOL2 format, chain Z [auth D] mmCIF format, chain L [auth A] mmCIF format, chain T [auth B] mmCIF format, chain Z [auth D]	L [auth A], T [auth B], Z [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain L [auth A] Focus chain T [auth B] Focus chain Z [auth D] Interactions & Density Focus chain L [auth A] Focus chain T [auth B] Focus chain Z [auth D]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain AA [auth D] SDF format, chain U [auth B] SDF format, chain X [auth C] MOL2 format, chain AA [auth D] MOL2 format, chain U [auth B] MOL2 format, chain X [auth C] mmCIF format, chain AA [auth D] mmCIF format, chain U [auth B] mmCIF format, chain X [auth C]	AA [auth D], U [auth B], X [auth C]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain AA [auth D] Focus chain U [auth B] Focus chain X [auth C] Interactions & Density Focus chain AA [auth D] Focus chain U [auth B] Focus chain X [auth C]