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Crystal structure of factor viia in complex with 1-(2,6- difluorophenyl)-3-[[3-[5-hydroxy-4-(1H-PYRROLO[3,2-C]PYRIDIN-2-yl) pyrazol-1-YL]PHENYL]METHYL]UREA

Analyse Crystal structure of factor viia in complex with 1-(2,6… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5PAX
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: 7ZP, CA, SO4, CL
Pockets: 3 · best druggability 0.47

Structure

x-ray diffraction · 2 distinct chains · 14% helix, 35% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Coagulation factor VII light chain (EC 3.4.21.21)	protein	58	17% helix, 28% strand	P08709
C	Coagulation factor VII heavy chain (EC 3.4.21.21)	protein	250	13% helix, 37% strand	P08709

Ligands and binding sites

7ZP · 1-(2,6-difluorophenyl)-3-[[3-[5-hydroxy-4-(1H-pyrrolo[3,2-c]pyridin-2-yl)pyrazol-1-yl]phenyl]methyl]urea · ligand · chains C
CA · Calcium ion · metal · chains C
SO4 · Sulfate ion · ion · 2 copies · chains C
CL · Chloride ion · ion · chains C
GOL · Glycerol · additive · 2 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	88	0.47	0.81	21	empty
2	110	0.46	0.79	29	7ZP
3	121	0.43	0.76	22	empty

Interfaces

1 interface between chains.

A–C · 1057 Å² buried · 15 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 disulfide (disulfide).

Compared structures

5PAX · 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 C against A, TM-score 0.97

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 5PAX · PDBe 5PAX · UniProt P08709

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