MolNFT v1 · #130347 · protein
Crystal structure of factor viia in complex with 1-(1- aminoisoquinolin-6-yl)-3-benzylurea
5PAJ · Coagulation factor VII light chain: “Crystal structure of factor viia in complex with 1-(1- aminoisoquinolin-6-yl)-3-benzylurea”. X-ray diffraction, 4 ligands (7XJ, CA, SO4), 2 pockets (best druggability 0.42). MolNFT v1 #130347 on…
- PDB
- 5PAJ
- Type
- protein
- Length
- 306 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
- 7XJ, CA, SO4, CL
- Pockets
- 2 · 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 | 56 | 16% helix, 29% strand | P08709 |
| B | Coagulation factor VII heavy chain (EC 3.4.21.21) | protein | 250 | 15% helix, 37% strand | P08709 |
Ligands and binding sites
- 7XJ · 1-(1-azanylisoquinolin-6-yl)-3-(phenylmethyl)urea · ligand · chains B
- CA · Calcium ion · metal · chains B
- SO4 · Sulfate ion · ion · 4 copies · chains B
- CL · Chloride ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 129 | 0.42 | 0.76 | 31 | 7XJ |
| 2 | 126 | 0.40 | 0.75 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 1032 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 5PAJ · Crystal Structure of Factor VIIa in complex with 1-(1-aminoisoquinolin-6-yl)-3-benzylurea · 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 0.98
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 5PAJ · PDBe 5PAJ · UniProt P08709
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