5PAR | pdb_00005par

Crystal Structure of Factor VIIa in complex with 1H-benzimidazol-2-amine

PDB DOI: https://doi.org/10.2210/pdb5PAR/pdb
Deposition Group: G_1002015 ExploreG_1002015

Classification: HYDROLASE/HYDROLASE INHIBITOR
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2016-11-10 Released: 2017-06-21
Deposition Author(s): Stihle, M., Mayweg, A., Roever, S., Rudolph, M.G.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.220 (Depositor), 0.220 (DCC)
R-Value Work:
0.182 (Depositor), 0.190 (DCC)
R-Value Observed:
0.184 (Depositor)

Starting Model: other
View more details

wwPDB Validation 3D Report Full Report

This is version 1.4 of the entry. See complete history.

Literature

Crystal Structure of a Factor VIIa complex

Mayweg, A., Roever, S., Rudolph, M.G.

To be published.

Macromolecule Content

Total Structure Weight: 36.11 kDa
Atom Count: 2,762
Modeled Residue Count: 308
Deposited Residue Count: 318
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Coagulation factor VII light chain	A	64	Homo sapiens	Mutation(s): 0 Gene Names: F7 EC: 3.4.21.21
UniProt & NIH Common Fund Data Resources
Find proteins for P08709 (Homo sapiens) Explore P08709 Go to UniProtKB: P08709
PHAROS: P08709 GTEx: ENSG00000057593
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P08709
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Coagulation factor VII heavy chain	B [auth C]	254	Homo sapiens	Mutation(s): 0 Gene Names: F7 EC: 3.4.21.21
UniProt & NIH Common Fund Data Resources
Find proteins for P08709 (Homo sapiens) Explore P08709 Go to UniProtKB: P08709
PHAROS: P08709 GTEx: ENSG00000057593
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P08709
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
AX7 Query on AX7 Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain L [auth C] SDF format, chain M [auth C] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain L [auth C] MOL2 format, chain M [auth C] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain L [auth C] mmCIF format, chain M [auth C]	C [auth A], D [auth A], L [auth C], M [auth C]	1H-benzimidazol-2-amine C₇ H₇ N₃ JWYUFVNJZUSCSM-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain L [auth C] Focus chain M [auth C] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain L [auth C] Focus chain M [auth C]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain K [auth C] SDF format, chain J [auth C] MOL2 format, chain K [auth C] MOL2 format, chain J [auth C] mmCIF format, chain K [auth C] mmCIF format, chain J [auth C]	J [auth C], K [auth C]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain J [auth C] Focus chain K [auth C] Interactions & Density Focus chain J [auth C] Focus chain K [auth C]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A]	E [auth A], F [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Interactions & Density Focus chain E [auth A] Focus chain F [auth A]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain G [auth C] MOL2 format, chain G [auth C] mmCIF format, chain G [auth C]	G [auth C]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain G [auth C] Interactions & Density Focus chain G [auth C]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain I [auth C] SDF format, chain H [auth C] MOL2 format, chain I [auth C] MOL2 format, chain H [auth C] mmCIF format, chain I [auth C] mmCIF format, chain H [auth C]	H [auth C], I [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain H [auth C] Focus chain I [auth C] Interactions & Density Focus chain H [auth C] Focus chain I [auth C]