MolNFT v1 · #130361 · protein
Crystal structure of factor viia in complex with 1-[[3-[5-hydroxy-4- (1H-PYRROLO[3,2-C]PYRIDIN-2-YL)PYRAZOL-1-YL]PHENYL]METHYL]-3- phenylurea
5PAY · Coagulation factor VII light chain: “Crystal structure of factor viia in complex with 1-[[3-[5-hydroxy-4…”. X-ray diffraction, 4 ligands (7ZY, CA, SO4), 2 pockets (best druggability 0.59). MolNFT v1 #130361 on GenesisL1: 3D…
- PDB
- 5PAY
- 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
- 7ZY, CA, SO4, CL
- Pockets
- 2 · best druggability 0.59
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 | 16% helix, 28% strand | P08709 |
| C | Coagulation factor VII heavy chain (EC 3.4.21.21) | protein | 250 | 14% helix, 37% strand | P08709 |
Ligands and binding sites
- 7ZY · 1-[[3-[5-hydroxy-4-(1H-pyrrolo[3,2-c]pyridin-2-yl) pyrazol-1-yl]phenyl]methyl]-3-phenylurea · ligand · chains C
- CA · Calcium ion · metal · chains C
- SO4 · Sulfate ion · ion · 2 copies · chains A, C
- CL · Chloride 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
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 215 | 0.59 | 0.80 | 39 | 7ZY |
| 2 | 137 | 0.41 | 0.74 | 20 | empty |
Interfaces
1 interface between chains.
- A–C · 1040 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
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 5PAY · PDBe 5PAY · UniProt P08709
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