Research workbench
Complex of thrombin with designed inhibitor 7165
Analyse Complex of thrombin with designed inhibitor 7165 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1VZQ
- Type
- protein
- Length
- 283 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thrombin heavy; Hirudin variant-2; Thrombin light
- EC
- 3.4.21.5
- UniProt
- P00734, P09945
- Ligands
- SHY, NA, CA
- Pockets
- 1 · best druggability 0.55
Structure
x-ray diffraction · 3 distinct chains · 17% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | Thrombin heavy (EC 3.4.21.5) | protein | 250 | 15% helix, 34% strand | P00734 |
| I | Hirudin variant-2 | protein | 6 | 0% helix, 0% strand | P09945 |
| L | Thrombin light (EC 3.4.21.5) | protein | 27 | 37% helix, 0% strand | P00734 |
Ligands and binding sites
- SHY · 4-[(3as,4r,7r,8as,8br)-2-(1,3-benzodioxol-5-ylmethyl)-7-hydroxy-1,3-dioxodecahydropyrrolo[3,4-a]pyrrolizin-4-yl]benzenecarboximidamide · ligand · chains H
- NA · Sodium ion · metal · chains H
- CA · Calcium ion · metal · chains H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 218 | 0.55 | 0.78 | 33 | SHY |
Interfaces
2 interfaces between chains.
- H–L · 1103 Ų buried · 27 hydrogen bonds · protein-protein
- H–I · 449 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 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 P00734
- Every structure of UniProt P09945
- Elsewhere: RCSB PDB 1VZQ · PDBe 1VZQ · UniProt P00734 · UniProt P09945
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