Research workbench
Crystal structure analysis of thrombin in complex with compound D58
Analyse Crystal structure analysis of thrombin in complex with compound D58 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4LXB
- Type
- protein
- Length
- 287 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Prothrombin, thrombin light chain; Hirudin variant-1; Prothrombin
- EC
- 3.4.21.5
- UniProt
- P00734, P01050
- Ligands
- 7R9, NAG, NA
- Pockets
- 1 · best druggability 0.60
Structure
x-ray diffraction · 3 distinct chains · 18% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | Prothrombin, thrombin light chain (EC 3.4.21.5) | protein | 250 | 15% helix, 36% strand | P00734 |
| I | Hirudin variant-1 | protein | 10 | 30% helix, 0% strand | P01050 |
| L | Prothrombin (EC 3.4.21.5) | protein | 27 | 37% helix, 0% strand | P00734 |
Ligands and binding sites
- 7R9 · 5-Chloro-thiophene-2-carboxylic acid [(S)-2-[2-difluoromethoxy-3-(2-oxo-piperidin-1-yl)-benzenesulfonylamino]-3-((S)-3-dimethylamino-pyrrolidin-1-yl)-3-oxo-propyl]-amide · ligand · chains H
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains H
- NA · Sodium ion · metal · 2 copies · 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 | 311 | 0.60 | 0.78 | 38 | 7R9 |
Interfaces
2 interfaces between chains.
- H–L · 1111 Ų buried · 26 hydrogen bonds · protein-protein
- H–I · 628 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 1 glycan, 1 modified (disulfide, N-glycosylation, sulfation).
Compared structures
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 P01050
- Elsewhere: RCSB PDB 4LXB · PDBe 4LXB · UniProt P00734 · UniProt P01050
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