MolNFT v1 · #130346 · protein
Human factor viia in complex with N-(2-amino-1H-benzimidazol-5-yl)-1- [3-[[(3,5-dimethyl-1,2-oxazol-4-YL)CARBAMOYLAMINO]METHYL]PHENYL]-5- hydroxypyrazole-4-carboxamide at 1.73A
5PAI · Coagulation factor VII light chain: “Human factor viia in complex with N-(2-amino-1H-benzimidazol-5-yl)-1…”. X-ray diffraction, 4 ligands (7YM, CA, SO4), 2 pockets (best druggability 0.53). MolNFT v1 #130346 on GenesisL1: 3D…
- PDB
- 5PAI
- Type
- protein
- Length
- 304 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
- 7YM, CA, SO4, CL
- Pockets
- 2 · best druggability 0.53
Structure
x-ray diffraction · 2 distinct chains · 14% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Coagulation factor VII light chain (EC 3.4.21.21) | protein | 57 | 18% helix, 28% strand | P08709 |
| B | Coagulation factor VII heavy chain (EC 3.4.21.21) | protein | 247 | 13% helix, 38% strand | P08709 |
Ligands and binding sites
- 7YM · N-(2-amino-1H-benzimidazol-5-yl)-1-[3-[[(3,5-dimethyl-1,2-oxazol-4-yl)carbamoylamino]methyl]phenyl]-5-hydroxypyrazole-4-carboxamide · ligand · chains B
- CA · Calcium ion · metal · chains B
- SO4 · Sulfate ion · ion · 2 copies · chains B
- CL · Chloride ion · ion · chains B
- GOL · Glycerol · additive · chains A
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 | 203 | 0.53 | 0.78 | 40 | 7YM |
| 2 | 130 | 0.43 | 0.76 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 1062 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 5PAI · human factor VIIa in complex with N-(2-amino-1H-benzimidazol-5-yl)-1-[3-[[(3,5-dimethyl-1… · 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 0.97
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 5PAI · PDBe 5PAI · UniProt P08709
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