Research workbench
Human factor viia in complex with 1-[[3-[5-hydroxy-3-methyl-4-(1H- PYRROLO[3,2-C]PYRIDIN-2-YL)PYRAZOL-1-YL]PHENYL]METHYL]-3-phenylurea at 2.43A
Analyse Human factor viia in complex with 1-[[3-[5-hydroxy-3-methyl-4-(1H… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5PB4
- 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
- 9RS, CA, CL, SO4
- Pockets
- 2 · best druggability 0.54
Structure
x-ray diffraction · 2 distinct chains · 14% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Coagulation factor VII light chain (EC 3.4.21.21) | protein | 57 | 14% helix, 25% strand | P08709 |
| C | Coagulation factor VII heavy chain (EC 3.4.21.21) | protein | 247 | 14% helix, 37% strand | P08709 |
Ligands and binding sites
- 9RS · N-({3-[5-hydroxy-3-methyl-4-(1H-pyrrolo[3,2-c]pyridin-2-yl)-1H-pyrazol-1-yl]phenyl}methyl)-N'-phenylurea · ligand · chains C
- CA · Calcium ion · metal · chains C
- CL · Chloride ion · ion · 2 copies · chains C
- SO4 · Sulfate ion · ion · 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
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 | 196 | 0.54 | 0.78 | 40 | 9RS |
| 2 | 120 | 0.41 | 0.76 | 20 | empty |
Interfaces
1 interface between chains.
- A–C · 1046 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 5PB4 · human factor VIIa in complex with 1-[[3-[5-hydroxy-3-methyl-4-(1H-pyrrolo[3,2-c]pyridin-2… · 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 5PB4 · PDBe 5PB4 · UniProt P08709
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