Research workbench
Novel covalent thrombin inhibitor from plant extract
Analyse Novel covalent thrombin inhibitor from plant extract in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1AWH
- Type
- protein
- Length
- 590 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alpha thrombin
- EC
- 3.4.21.5
- UniProt
- P00734
- Ligands
- GR3
- Pockets
- 8 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 16% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Alpha thrombin (EC 3.4.21.5) | protein | 36 | 25% helix, 0% strand | P00734 |
| B, D | Alpha thrombin (EC 3.4.21.5) | protein | 259 | 14% helix, 34% strand | P00734 |
Ligands and binding sites
- GR3 · 3-acetoxy-17-(1-formyl-5-methyl-3-oxo-hex-4-enyl)-16-hydroxy-4,10,13,14-tetramethyl-2,3,4,5,6,9,10,11,12,13,14,15,16,17-tetradecahydro-1H-cyclopenta[a]phenanthrene-4-carboxylic acid · ligand · 2 copies · chains B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 962 | 0.80 | 0.82 | 85 | GR3 |
| 2 | 377 | 0.63 | 0.78 | 52 | GR3 |
| 3 | 50 | 0.62 | 0.94 | 20 | empty |
| 4 | 55 | 0.56 | 0.90 | 17 | empty |
| 5 | 144 | 0.53 | 0.80 | 19 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1385 Ų buried · 31 hydrogen bonds · protein-protein
- C–D · 1366 Ų buried · 34 hydrogen bonds · protein-protein
- B–D · 501 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 2 covalent (disulfide, covalent ligand).
Compared structures
- 1AWH · Novel covalent thrombin inhibitor from plant extract · the same entry in another collection · chain B against B, TM-score 1.00
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
- Elsewhere: RCSB PDB 1AWH · PDBe 1AWH · UniProt P00734
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