MolNFT v1 · #130338 · protein
Crystal structure of factor viia in complex with cyclohexylmethanamine
5PAA · Coagulation factor VII light chain: “Crystal structure of factor viia in complex with cyclohexylmethanamine”. X-ray diffraction, 4 ligands (AMC, CA, CL), 3 pockets (best druggability 0.42). MolNFT v1 #130338 on GenesisL1: 3D…
- PDB
- 5PAA
- 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
- AMC, CA, CL, 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 | 17% 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
- AMC · Aminomethylcyclohexane · ligand · chains C
- CA · Calcium ion · metal · chains C
- CL · Chloride ion · ion · 4 copies · chains C
- SO4 · Sulfate ion · ion · 3 copies · 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.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 141 | 0.42 | 0.75 | 27 | AMC, SO4 |
| 2 | 127 | 0.41 | 0.75 | 20 | empty |
| 3 | 56 | 0.39 | 0.80 | 15 | empty |
Interfaces
1 interface between chains.
- A–C · 1045 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 5PAA · Crystal Structure of Factor VIIa in complex with cyclohexylmethanamine · 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 5PAA · PDBe 5PAA · UniProt P08709
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