Research workbench
Coagulation factor VII zymogen (EGF2/PROTEASE) in complex with inhibitory exosite peptide a-183
Analyse Coagulation factor VII zymogen (EGF2/PROTEASE) in complex with inhibitory… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1JBU
- Type
- protein
- Length
- 308 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Coagulation factor VII; Peptide exosite inhibitor a-183
- EC
- 3.4.21.21
- UniProt
- P08709
- Ligands
- BEN, SO4
- Pockets
- 4 · best druggability 0.56
Structure
x-ray diffraction · 3 distinct chains · 18% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | Coagulation factor VII (EC 3.4.21.21) | protein | 239 | 19% helix, 38% strand | P08709 |
| L | Coagulation factor VII (EC 3.4.21.21) | protein | 54 | 15% helix, 22% strand | P08709 |
| X | Peptide exosite inhibitor a-183 | protein | 15 | 0% helix, 27% strand | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 138 | 0.56 | 0.82 | 24 | empty |
| 2 | 61 | 0.44 | 0.82 | 17 | empty |
| 3 | 124 | 0.40 | 0.75 | 20 | empty |
| 4 | 69 | 0.30 | 0.74 | 20 | empty |
Interfaces
2 interfaces between chains.
- H–L · 1006 Ų buried · 13 hydrogen bonds · protein-protein
- H–X · 944 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 disulfide (disulfide).
Compared structures
- 1JBU · Coagulation Factor VII Zymogen (EGF2/Protease) in Complex with Inhibitory Exosite Peptide… · the same entry in another collection · chain H against H, TM-score 1.00
- P08709 · AlphaFold monomer V2.0 prediction for coagulation factor VII (P08709) · a predicted model of the same protein · chain L against A, TM-score 0.96
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 1JBU · PDBe 1JBU · UniProt P08709
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