MolNFT v1 · #130339 · protein
Crystal structure of factor viia in complex with 1-[[3-[2-hydroxy-3- (1H-PYRROLO[3,2-C]PYRIDIN-2-YL)PHENYL]PHENYL]METHYL]-3-phenylurea
5PAB · Coagulation factor VII heavy chain: “Crystal structure of factor viia in complex with 1-[[3-[2-hydroxy-3…”. X-ray diffraction, 4 ligands (7XD, CA, CL), 2 pockets (best druggability 0.52). MolNFT v1 #130339 on GenesisL1: 3D…
- PDB
- 5PAB
- Type
- protein
- Length
- 303 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Coagulation factor VII heavy chain; Coagulation factor VII light chain
- EC
- 3.4.21.21
- UniProt
- P08709
- Ligands
- 7XD, CA, CL, SO4
- Pockets
- 2 · best druggability 0.52
Structure
x-ray diffraction · 2 distinct chains · 14% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | Coagulation factor VII heavy chain (EC 3.4.21.21) | protein | 248 | 14% helix, 38% strand | P08709 |
| L | Coagulation factor VII light chain (EC 3.4.21.21) | protein | 55 | 15% helix, 29% strand | P08709 |
Ligands and binding sites
- 7XD · 1-[[3-[2-oxidanyl-3-(1~{H}-pyrrolo[3,2-c]pyridin-2-yl) phenyl]phenyl]methyl]-3-phenyl-urea · ligand · chains H
- CA · Calcium ion · metal · chains H
- CL · Chloride ion · ion · 3 copies · chains H
- SO4 · Sulfate ion · ion · 2 copies · chains H, L
- GOL · Glycerol · additive · 4 copies · chains H, L
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 | 216 | 0.52 | 0.77 | 36 | 7XD, GOL |
| 2 | 114 | 0.45 | 0.78 | 18 | empty |
Interfaces
1 interface between chains.
- H–L · 1044 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 1 modified (disulfide, oxidation).
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 5PAB · PDBe 5PAB · UniProt P08709
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.