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
- 1DWD
- Type
- protein
- Length
- 296 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alpha-thrombin (small subunit); Alpha-thrombin (large subunit); Hirudin iiia
- EC
- 3.4.21.5
- UniProt
- P00734, P28508
- Ligands
- MID
- Pockets
- 2 · best druggability 0.57
Structure
x-ray diffraction · 3 distinct chains · 14% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | Alpha-thrombin (small subunit) (EC 3.4.21.5) | protein | 29 | 31% helix, 0% strand | P00734 |
| H | Alpha-thrombin (large subunit) (EC 3.4.21.5) | protein | 257 | 11% helix, 35% strand | P00734 |
| I | Hirudin iiia | protein | 10 | 30% helix, 0% strand | P28508 |
Ligands and binding sites
- MID · 1-[N-(naphthalen-2-ylsulfonyl)glycyl-4-carbamimidoyl-D-phenylalanyl]piperidine · ligand · chains H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 288 | 0.57 | 0.77 | 43 | MID |
| 2 | 170 | 0.45 | 0.75 | 22 | empty |
Interfaces
2 interfaces between chains.
- L–H · 1111 Ų buried · 24 hydrogen bonds · protein-protein
- H–I · 602 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 1DWD · Crystallographic analysis at 3.0-ångströms resolution of the binding to human thrombin of… · the same entry in another collection · chain H against H, 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 0.91
- P28508 · AlphaFold monomer V2.0 prediction for hirudin-3A' (P28508) · a predicted model of the same protein · chain I against A, TM-score 0.49
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 P28508
- Elsewhere: RCSB PDB 1DWD · PDBe 1DWD · UniProt P00734 · UniProt P28508
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.