Research workbench
Crystallographic analysis at 3.0-ångströms resolution of the binding to human thrombin of four active site-directed inhibitors
Analyse Crystallographic analysis at 3.0-ångströms resolution of the binding to human… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1DWE
- Type
- protein
- Length
- 296 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alpha-thrombin light chain; Alpha-thrombin heavy chain; Hirudin iiia
- EC
- 3.4.21.5
- UniProt
- P00734, P28507
- Ligands
- 0G6
- Pockets
- 3 · best druggability 0.56
Structure
x-ray diffraction · 3 distinct chains · 14% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | Alpha-thrombin light chain (EC 3.4.21.5) | protein | 28 | 32% helix, 0% strand | P00734 |
| H | Alpha-thrombin heavy chain (EC 3.4.21.5) | protein | 257 | 13% helix, 35% strand | P00734 |
| I | Hirudin iiia | protein | 11 | 0% helix, 0% strand | P28507 |
Ligands and binding sites
- 0G6 · D-phenylalanyl-N-[(2S,3S)-6-{[amino(iminio)methyl]amino}-1-chloro-2-hydroxyhexan-3-yl]-L-prolinamide · ligand · chains H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 231 | 0.56 | 0.78 | 40 | 0G6 |
| 2 | 148 | 0.44 | 0.75 | 17 | empty |
| 3 | 52 | 0.29 | 0.75 | 16 | empty |
Interfaces
2 interfaces between chains.
- L–H · 1122 Ų buried · 21 hydrogen bonds · protein-protein
- H–I · 584 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 2 covalent (disulfide, covalent ligand).
Compared structures
- 1DWE · Crystallographic analysis at 3.0-Angstroms resolution of the binding to human thrombin of… · the same entry in another collection · chain L against L, TM-score 1.00
- P00734 · AlphaFold monomer V2.0 prediction for prothrombin (P00734) · a predicted model of the same protein · chain H against A, TM-score 0.90
- P28507 · AlphaFold monomer V2.0 prediction for hirudin-3A (P28507) · a predicted model of the same protein · chain I against A, TM-score 0.45
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 P28507
- Elsewhere: RCSB PDB 1DWE · PDBe 1DWE · UniProt P00734 · UniProt P28507
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.