MolNFT v1 · #130357 · protein

Crystal structure of factor viia in complex with N-(2-amino-1H- benzimidazol-5-yl)-2-[3-[(2-amino-2-oxoethyl)- METHYLSULFONYLAMINO]PHENYL]ACETAMIDE;2,2,2-trifluoroacetic acid

5PAU · Coagulation factor VII light chain: “Crystal structure of factor viia in complex with N-(2-amino-1H…”. X-ray diffraction, 4 ligands (7ZJ, CA, CL), 3 pockets (best druggability 0.42). MolNFT v1 #130357 on GenesisL1: 3D structure…

PDB: 5PAU
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: 7ZJ, CA, CL, SO4
Pockets: 3 · best druggability 0.42

Structure

x-ray diffraction · 2 distinct chains · 15% helix, 36% 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
C	Coagulation factor VII heavy chain (EC 3.4.21.21)	protein	250	14% helix, 38% strand	P08709

Ligands and binding sites

7ZJ · N-(2-amino-1H-benzimidazol-5-yl)-2-[3-[(2-amino-2-oxoethyl)-methylsulfonylamino]phenyl]acetamide · ligand · chains C
CA · Calcium ion · metal · chains C
CL · Chloride ion · ion · 2 copies · chains C
SO4 · Sulfate ion · ion · 2 copies · chains C
GOL · Glycerol · additive · 3 copies · chains A, C

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	136	0.42	0.76	30	SO4, 7ZJ
2	121	0.42	0.76	19	empty
3	64	0.42	0.81	14	GOL

Interfaces

1 interface between chains.

A–C · 1053 Å² buried · 15 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 disulfide (disulfide).

Compared structures

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

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