MolNFT v1 · #24160 · protein
Alpha-thrombin (hirugen) complexed with na-(N,N-dimethylcarbamoyl)- alpha-azalysine
1UMA: “Alpha-thrombin (hirugen) complexed with na-(N,N-dimethylcarbamoyl)- alpha-azalysine”. X-ray diffraction, 2 ligands (IN2, NAG), 1 pocket (best druggability 0.56). MolNFT v1 #24160 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 1UMA
- Type
- protein
- Length
- 299 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alpha-thrombin; Hirudin I
- EC
- 3.4.21.5
- UniProt
- P00734, P28501
- Ligands
- IN2, NAG
- Pockets
- 1 · best druggability 0.56
Structure
x-ray diffraction · 3 distinct chains · 17% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | Alpha-thrombin (EC 3.4.21.5) | protein | 36 | 28% helix, 6% strand | P00734 |
| H | Alpha-thrombin (EC 3.4.21.5) | protein | 253 | 15% helix, 35% strand | P00734 |
| I | Hirudin I | protein | 10 | 30% helix, 0% strand | P28501 |
Ligands and binding sites
- IN2 · N,N-dimethylcarbamoyl-alpha-azalysine · ligand · 2 copies · chains H
- 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 317 | 0.56 | 0.76 | 42 | IN2 |
Interfaces
2 interfaces between chains.
- L–H · 1488 Ų buried · 37 hydrogen bonds · protein-protein
- H–I · 640 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 1 covalent, 1 glycan, 1 modified (disulfide, covalent ligand, N-glycosylation, sulfation).
Compared structures
- 1UMA · Alpha-thrombin (hirugen) complexed with na-(N,N-dimethylcarbamoyl)-alpha-azalysine · the same entry in another collection · chain H against H, 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 P28501
- Elsewhere: RCSB PDB 1UMA · PDBe 1UMA · UniProt P00734 · UniProt P28501
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