MolNFT v1 · #63318 · protein
Thrombin inhibition
3F68 · Prothrombin: “Thrombin inhibition”. X-ray diffraction, 2 ligands (91U, NA), 2 pockets (best druggability 0.54). MolNFT v1 #63318 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3F68
- Type
- protein
- Length
- 285 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
- 91U, NA
- Pockets
- 2 · best druggability 0.54
Structure
x-ray diffraction · 3 distinct chains · 18% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | Prothrombin (EC 3.4.21.5) | protein | 27 | 37% helix, 0% strand | P00734 |
| H | Prothrombin (EC 3.4.21.5) | protein | 249 | 16% helix, 36% strand | P00734 |
| I | Hirudin variant-2 | protein | 9 | 0% helix, 0% strand | P09945 |
Ligands and binding sites
- 91U · N-acetyl-3-cyclohexyl-D-alanyl-N-(3-chlorobenzyl)-L-prolinamide · ligand · 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
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 260 | 0.54 | 0.76 | 37 | 91U |
| 2 | 51 | 0.26 | 0.73 | 14 | empty |
Interfaces
2 interfaces between chains.
- L–H · 1091 Ų buried · 28 hydrogen bonds · protein-protein
- H–I · 562 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 1 modified (disulfide, sulfation).
Compared structures
- 3F68 · Thrombin Inhibition · 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 3F68 · PDBe 3F68 · UniProt P00734 · UniProt P09945
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