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
- 1DWC
- 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
- MIT
- Pockets
- 2 · best druggability 0.57
Structure
x-ray diffraction · 3 distinct chains · 14% helix, 29% 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 | 13% helix, 34% strand | P00734 |
| I | Hirudin iiia | protein | 10 | 0% helix, 0% strand | P28508 |
Ligands and binding sites
- MIT · amino{[(4S)-5-[(2R,4R)-2-carboxy-4-methylpiperidin-1-yl]-4-({[(3R)-3-methyl-1,2,3,4-tetrahydroquinolin-8-yl]sulfonyl}amino)-5-oxopentyl]amino}methaniminium · 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 | 290 | 0.57 | 0.77 | 39 | MIT |
| 2 | 152 | 0.43 | 0.75 | 19 | empty |
Interfaces
2 interfaces between chains.
- L–H · 1116 Ų buried · 23 hydrogen bonds · protein-protein
- H–I · 610 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 1DWC · Crystallographic analysis at 3.0-ångströms 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 0.91
- 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 1DWC · PDBe 1DWC · UniProt P00734 · UniProt P28508
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.