Research workbench
Crystal structure of thrombin in complex with compound 1
Analyse Crystal structure of thrombin in complex with compound 1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1TA2
- Type
- protein
- Length
- 287 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thrombin; Hirudin
- EC
- 3.4.21.5
- UniProt
- P00734, P28504
- Ligands
- 176
- Pockets
- 1 · best druggability 0.50
Structure
x-ray diffraction · 2 distinct chains · 16% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Thrombin (EC 3.4.21.5) | protein | 276 | 17% helix, 32% strand | P00734 |
| B | Hirudin | protein | 11 | 0% helix, 0% strand | P28504 |
Ligands and binding sites
- 176 · 1-(2-amino-3,3-diphenyl-propionyl)-pyrrolidine-3-carboxylic acid 2,5-dichloro-benzylamide · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 191 | 0.50 | 0.76 | 34 | 176 |
Interfaces
1 interface between chains.
- A–B · 683 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 1 modified (disulfide, sulfation).
Compared structures
- 1TA2 · Crystal structure of thrombin in complex with compound 1 · the same entry in another collection · chain A against A, TM-score 1.00
- P00734 · AlphaFold monomer V2.0 prediction for prothrombin (P00734) · a predicted model of the same protein · chain A against A, TM-score 0.92
- P28504 · AlphaFold monomer V2.0 prediction for hirudin-2 (P28504) · a predicted model of the same protein · chain B against A, TM-score 0.52
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 P28504
- Elsewhere: RCSB PDB 1TA2 · PDBe 1TA2 · UniProt P00734 · UniProt P28504
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.