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
- 1AWF
- Type
- protein
- Length
- 295 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alpha thrombin; Hirugen
- EC
- 3.4.21.5
- UniProt
- P00734, P28501
- Ligands
- GR4
- Pockets
- 1 · best druggability 0.64
Structure
x-ray diffraction · 3 distinct chains · 16% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | Alpha thrombin (EC 3.4.21.5) | protein | 27 | 37% helix, 0% strand | P00734 |
| H | Alpha thrombin (EC 3.4.21.5) | protein | 258 | 13% helix, 35% strand | P00734 |
| I | Hirugen | protein | 10 | 30% helix, 0% strand | P28501 |
Ligands and binding sites
- GR4 · R3-acetoxy-17-(1-formyl-5-methyl-3-oxo-hex-4-enyl)-12,16-dihydroxy-14-hydroxymethyl-4,10,13-trimethyl-2,3,4,5,6,9,10,11,12,13,14,15,16,17-tetradecahydro-1H-cyclopenta[a]phenanthrene-4-carboxylic acid idopyranosyl ester · ligand · chains H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 339 | 0.64 | 0.80 | 43 | GR4 |
Interfaces
2 interfaces between chains.
- L–H · 1143 Ų buried · 24 hydrogen bonds · protein-protein
- H–I · 640 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 1 covalent, 1 modified (disulfide, covalent ligand, sulfation).
Compared structures
- 1AWF · Novel covalent thrombin inhibitor from plant extract · the same entry in another collection · chain L against L, 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
- Every structure of UniProt P28501
- Elsewhere: RCSB PDB 1AWF · PDBe 1AWF · UniProt P00734 · UniProt P28501
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