MolNFT v1 · #96964 · protein
Structure of factor viia in complex with the inhibitor 2-{2-[(4- CARBAMIMIDOYLPHENYL)CARBAMOYL]-6-methoxypyridin-3-yl}-5-{[(2S)-1- hydroxy-3,3-dimethylbutan-2-YL]CARBAMOYL}BENZOIC acid
4JZD · Factor viia (heavy chain): “Structure of factor viia in complex with the inhibitor 2-{2-[(4…”. X-ray diffraction, 3 ligands (1NJ, CA, SO4), 4 pockets (best druggability 0.45). MolNFT v1 #96964 on GenesisL1: 3D structure, binding…
- PDB
- 4JZD
- Type
- protein
- Length
- 309 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Factor viia (heavy chain); Factor viia (light chain)
- EC
- 3.4.21.21
- UniProt
- P08709
- Ligands
- 1NJ, CA, SO4
- Pockets
- 4 · best druggability 0.45
Structure
x-ray diffraction · 2 distinct chains · 14% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | Factor viia (heavy chain) (EC 3.4.21.21) | protein | 254 | 14% helix, 37% strand | P08709 |
| L | Factor viia (light chain) (EC 3.4.21.21) | protein | 55 | 15% helix, 25% strand | P08709 |
Ligands and binding sites
- 1NJ · 2-{2-[(4-carbamimidoylphenyl)carbamoyl]-6-methoxypyridin-3-yl}-5-{[(2S)-1-hydroxy-3,3-dimethylbutan-2-yl]carbamoyl}benzoic acid · ligand · 2 copies · chains H
- CA · Calcium ion · metal · chains H
- SO4 · Sulfate ion · ion · 6 copies · chains H, L
- GOL · Glycerol · additive · chains H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 67 | 0.45 | 0.82 | 17 | empty |
| 2 | 140 | 0.43 | 0.76 | 30 | 1NJ, GOL |
| 3 | 114 | 0.41 | 0.76 | 20 | empty |
| 4 | 53 | 0.27 | 0.74 | 15 | SO4 |
Interfaces
1 interface between chains.
- H–L · 1034 Ų buried · 16 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 4JZD · PDBe 4JZD · UniProt P08709
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