MolNFT v1 · #106039 · protein
Structure of prethrombin-2 mutant S195A bound to the active site inhibitor argatroban
4RN6 · Thrombin heavy chain: “Structure of prethrombin-2 mutant S195A bound to the active site inhibitor argatroban”. X-ray diffraction, 1 ligand (15U), 9 pockets (best druggability 0.71). MolNFT v1 #106039 on GenesisL1: 3D structure…
- PDB
- 4RN6
- Type
- protein
- Length
- 568 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thrombin heavy chain
- EC
- 3.4.21.5
- UniProt
- P00734
- Ligands
- 15U
- Pockets
- 9 · best druggability 0.71
Structure
x-ray diffraction · 1 distinct chain · 18% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Thrombin heavy chain (EC 3.4.21.5) | protein | 284 | 18% helix, 27% 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 A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 524 | 0.71 | 0.80 | 67 | 15U |
| 2 | 408 | 0.67 | 0.80 | 52 | 15U |
| 3 | 63 | 0.56 | 0.88 | 15 | empty |
| 4 | 54 | 0.54 | 0.89 | 16 | empty |
| 5 | 104 | 0.51 | 0.82 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 693 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 4RN6 · Structure of prethrombin-2 mutant s195a bound to the active site inhibitor argatroban · the same entry in another collection · chain B against B, TM-score 1.00
- P00734 · AlphaFold monomer V2.0 prediction for prothrombin (P00734) · a predicted model of the same protein · chain B against A, TM-score 0.93
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 4RN6 · PDBe 4RN6 · UniProt P00734
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