MolNFT v1 · #25846 · protein
Alpha-thrombin complex with sulfated hirudin (residues 54-65) and L- arginine template inhibitor CS107
1W7G: “Alpha-thrombin complex with sulfated hirudin (residues 54-65) and L- arginine template inhibitor CS107”. X-ray diffraction, 1 ligand (MIU), 2 pockets (best druggability 0.58). MolNFT v1 #25846 on GenesisL1: 3D structure, binding…
- PDB
- 1W7G
- Type
- protein
- Length
- 286 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thrombin; Hirudin I
- EC
- 3.4.21.5
- UniProt
- P00734, P09945
- Ligands
- MIU
- Pockets
- 2 · best druggability 0.58
Structure
x-ray diffraction · 3 distinct chains · 17% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | Thrombin (EC 3.4.21.5) | protein | 252 | 15% helix, 34% strand | P00734 |
| I | Hirudin I | protein | 8 | 0% helix, 0% strand | P09945 |
| L | Thrombin (EC 3.4.21.5) | protein | 26 | 38% helix, 0% strand | P00734 |
Ligands and binding sites
- MIU · N-{(1S)-1-{[4-(3-aminopropyl)piperazin-1-yl]carbonyl}-4-[(diaminomethylene)amino]butyl}-3-(trifluoromethyl)benzenesulfonamide · ligand · 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 | 274 | 0.58 | 0.78 | 40 | MIU |
| 2 | 70 | 0.37 | 0.78 | 21 | empty |
Interfaces
2 interfaces between chains.
- H–L · 1088 Ų buried · 28 hydrogen bonds · protein-protein
- H–I · 526 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 1W7G · Alpha-thrombin complex with sulfated hirudin (residues 54-65) and L- Arginine template… · the same entry in another collection · chain H against H, TM-score 1.00
- P09945 · AlphaFold monomer V2.0 prediction for hirudin variant-2 (P09945) · a predicted model of the same protein · chain I against A, TM-score 0.54
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 1W7G · PDBe 1W7G · UniProt P00734 · UniProt P09945
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