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Crystal structure of factor viia in complex with N-(2-amino-1H- benzimidazol-5-yl)-2-(3-CHLOROPHENYL)ACETAMIDE

Analyse Crystal structure of factor viia in complex with N-(2-amino-1H… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5PAT
Type: protein
Length: 308 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Coagulation factor VII light chain; Coagulation factor VII heavy chain
EC: 3.4.21.21
UniProt: P08709
Ligands: 7ZG, SO4
Pockets: 3 · best druggability 0.42

Structure

x-ray diffraction · 2 distinct chains · 15% helix, 35% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Coagulation factor VII light chain (EC 3.4.21.21)	protein	58	19% helix, 28% strand	P08709
B	Coagulation factor VII heavy chain (EC 3.4.21.21)	protein	250	14% helix, 37% strand	P08709

Ligands and binding sites

7ZG · N-(2-amino-1H-benzimidazol-5-yl)-2-(3-chlorophenyl) acetamide · ligand · chains B
SO4 · Sulfate ion · ion · 2 copies · chains B

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	143	0.42	0.75	33	7ZG, SO4
2	139	0.42	0.75	21	empty
3	53	0.40	0.81	13	empty

Interfaces

1 interface between chains.

A–B · 1045 Å² buried · 15 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 disulfide (disulfide).

Compared structures

5PAT · Crystal Structure of Factor VIIa in complex with… · the same entry in another collection · chain A against A, TM-score 1.00
P08709 · AlphaFold monomer V2.0 prediction for coagulation factor VII (P08709) · a predicted model of the same protein · chain B against A, TM-score 0.98

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt P08709
Elsewhere: RCSB PDB 5PAT · PDBe 5PAT · UniProt P08709

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