MolNFT v1 · #94321 · protein
The refined structure of the hirudin-thrombin complex
4HTC · Alpha-thrombin (small subunit): “The refined structure of the hirudin-thrombin complex”. X-ray diffraction, 1 ligand (NAG), 4 pockets (best druggability 0.71). MolNFT v1 #94321 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 4HTC
- Type
- protein
- Length
- 351 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alpha-thrombin (small subunit); Alpha-thrombin (large subunit); Hirudin variant 2
- EC
- 3.4.21.5
- UniProt
- P00734, P09945
- Ligands
- NAG
- Pockets
- 4 · best druggability 0.71
Structure
x-ray diffraction · 3 distinct chains · 14% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | Alpha-thrombin (small subunit) (EC 3.4.21.5) | protein | 33 | 33% helix, 0% strand | P00734 |
| H | Alpha-thrombin (large subunit) (EC 3.4.21.5) | protein | 257 | 14% helix, 35% strand | P00734 |
| I | Hirudin variant 2 | protein | 61 | 5% helix, 31% strand | P09945 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 73 | 0.71 | 0.96 | 30 | empty |
| 2 | 207 | 0.47 | 0.74 | 24 | empty |
| 3 | 67 | 0.38 | 0.79 | 21 | empty |
| 4 | 51 | 0.37 | 0.80 | 13 | empty |
Interfaces
2 interfaces between chains.
- H–I · 1794 Ų buried · 26 hydrogen bonds · protein-protein
- L–H · 1172 Ų buried · 22 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 4HTC · The refined structure of the hirudin-thrombin complex · 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 4HTC · PDBe 4HTC · UniProt P00734 · UniProt P09945
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