Research workbench
Structure of thrombin mutant S195A bound to the active site inhibitor argatroban
Analyse Structure of thrombin mutant S195A bound to the active site inhibitor argatroban in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4HFP
- Type
- protein
- Length
- 573 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Prothrombin
- EC
- 3.4.21.5
- UniProt
- P00734
- Ligands
- 15U, NA
- Pockets
- 7 · best druggability 0.66
Structure
x-ray diffraction · 3 distinct chains · 13% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Prothrombin (EC 3.4.21.5) | protein | 29 | 21% helix, 0% strand | P00734 |
| B, D | Prothrombin (EC 3.4.21.5) | protein | 257 | 10% helix, 33% strand | P00734 |
| C | Prothrombin (EC 3.4.21.5) | protein | 30 | 27% helix, 0% strand | P00734 |
Ligands and binding sites
- 15U · (2R,4R)-4-methyl-1-(N~2~-{[(3S)-3-methyl-1,2,3,4-tetrahydroquinolin-8-yl]sulfonyl}-L-arginyl)piperidine-2-carboxylic acid · ligand · 2 copies · chains B, D
- NA · Sodium ion · metal · 2 copies · chains B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 304 | 0.66 | 0.82 | 41 | 15U |
| 2 | 376 | 0.63 | 0.78 | 45 | 15U |
| 3 | 113 | 0.58 | 0.86 | 29 | empty |
| 4 | 92 | 0.37 | 0.75 | 17 | empty |
| 5 | 67 | 0.36 | 0.77 | 17 | empty |
Interfaces
6 interfaces between chains.
- A–B · 1208 Ų buried · 23 hydrogen bonds · protein-protein
- C–D · 1204 Ų buried · 24 hydrogen bonds · protein-protein
- A–D · 350 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 211 Ų buried · 1 hydrogen bond · protein-protein
- A–C · 156 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 4HFP · Structure of thrombin mutant S195a bound to the active site inhibitor argatroban · the same entry in another collection · chain D against D, TM-score 1.00
- P00734 · AlphaFold monomer V2.0 prediction for prothrombin (P00734) · a predicted model of the same protein · chain D against A, TM-score 0.91
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 4HFP · PDBe 4HFP · UniProt P00734
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