Research workbench
Crystal structure of thrombin in complex with a novel glucose- conjugated potent inhibitor
Analyse Crystal structure of thrombin in complex with a novel glucose- conjugated… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6EO8
- Type
- protein
- Length
- 283 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Prothrombin; Hirudin variant-2
- EC
- 3.4.21.5
- UniProt
- P00734, P09945
- Ligands
- 2FN
- Pockets
- 1 · best druggability 0.59
Structure
x-ray diffraction · 3 distinct chains · 16% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | Prothrombin (EC 3.4.21.5) | protein | 26 | 38% helix, 0% strand | P00734 |
| H | Prothrombin (EC 3.4.21.5) | protein | 247 | 14% helix, 36% strand | P00734 |
| I | Hirudin variant-2 | protein | 10 | 0% helix, 0% strand | P09945 |
Ligands and binding sites
- 2FN · N-(2-{[5-(5-chlorothiophen-2-yl)-1,2-oxazol-3-yl]methoxy}-6-[3-(beta-D-glucopyranosyloxy) propoxy]phenyl)-1-(propan-2-yl)piperidine-4-carboxamide · ligand · chains H
- DMS · Dimethyl sulfoxide · additive · 6 copies · chains L, 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 | 245 | 0.59 | 0.80 | 37 | DMS, 2FN |
Interfaces
2 interfaces between chains.
- L–H · 1112 Ų buried · 27 hydrogen bonds · protein-protein
- H–I · 639 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 1 modified (disulfide, sulfation).
Compared structures
- 6EO8 · Crystal structure of thrombin in complex with a novel glucose-conjugated potent inhibitor · 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 P09945
- Elsewhere: RCSB PDB 6EO8 · PDBe 6EO8 · UniProt P00734 · UniProt P09945
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