MolNFT v1 · #106605 · protein
The crystal structure of alpha-thrombin-hirunorm IV complex reveals a novel specificity site recognition mode.
4THN: “The crystal structure of alpha-thrombin-hirunorm IV complex reveals a novel specificity site recognition mode.”. X-ray diffraction, 1 ligand (NAG), 1 pocket (best druggability 0.42). MolNFT v1 #106605 on GenesisL1: 3D structure…
- PDB
- 4THN
- Type
- protein
- Length
- 303 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alpha-thrombin; Hirunorm IV
- EC
- 3.4.21.5
- UniProt
- P00734
- Ligands
- NAG
- Pockets
- 1 · best druggability 0.42
Structure
x-ray diffraction · 3 distinct chains · 17% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | Alpha-thrombin (EC 3.4.21.5) | protein | 36 | 28% helix, 8% strand | P00734 |
| H | Alpha-thrombin (EC 3.4.21.5) | protein | 253 | 16% helix, 36% strand | P00734 |
| I | Hirunorm IV | protein | 14 | 21% helix, 7% strand | — |
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
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 137 | 0.42 | 0.75 | 21 | empty |
Interfaces
2 interfaces between chains.
- L–H · 1442 Ų buried · 31 hydrogen bonds · protein-protein
- H–I · 1088 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 modified, 4 disulfide, 1 d-amino, 1 glycan (nonstandard, disulfide, D-amino acid, N-glycosylation).
Compared structures
- 4THN · The crystal structure of alpha-thrombin-hirunorm IV complex reveals a novel specificity… · 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
- Elsewhere: RCSB PDB 4THN · PDBe 4THN · UniProt P00734
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