Research workbench
Crystal structure of active site-inhibited human coagulation factor viia (des-gla)
Analyse Crystal structure of active site-inhibited human coagulation factor viia… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1CVW
- Type
- protein
- Length
- 309 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Coagulation factor viia (light chain) (des-gla); Coagulation factor viia (heavy chain)…
- EC
- 3.4.21.21
- UniProt
- P08709
- Ligands
- 0GE, CA
- Pockets
- 4 · best druggability 0.47
Structure
x-ray diffraction · 2 distinct chains · 13% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | Coagulation factor viia (light chain) (des-gla) (EC 3.4.21.21) | protein | 55 | 15% helix, 29% strand | P08709 |
| H | Coagulation factor viia (heavy chain) (des-gla) (EC 3.4.21.21) | protein | 254 | 13% helix, 37% strand | P08709 |
Ligands and binding sites
- 0GE · N-{[5-(dimethylamino)naphthalen-1-yl]sulfonyl}-L-alpha-glutamyl-N-[(2S,3S)-6-carbamimidamido-1-chloro-2-hydroxyhexan-3-yl]glycinamide · ligand · chains H
- CA · Calcium ion · metal · 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 | 95 | 0.47 | 0.81 | 20 | empty |
| 2 | 118 | 0.43 | 0.77 | 28 | 0GE |
| 3 | 98 | 0.37 | 0.75 | 15 | empty |
| 4 | 62 | 0.29 | 0.75 | 15 | empty |
Interfaces
1 interface between chains.
- L–H · 1044 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 disulfide, 2 covalent (disulfide, covalent ligand).
Compared structures
- 1CVW · Crystal structure of active site-inhibited human coagulation factor VIIA (DES-GLA) · the same entry in another collection · chain L against L, TM-score 1.00
- P08709 · AlphaFold monomer V2.0 prediction for coagulation factor VII (P08709) · a predicted model of the same protein · chain H 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 1CVW · PDBe 1CVW · UniProt P08709
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