MolNFT v1 · #139823 · protein
Crystal structure of da-36, a thrombin-like enzyme from deinagkistrodon acutus
5XRF · Snake venom serine protease da-36: “Crystal structure of da-36, a thrombin-like enzyme from deinagkistrodon acutus”. X-ray diffraction, 4 ligands (NAG, BMA, FUC), 1 pocket (best druggability 0.36). MolNFT v1 #139823 on GenesisL1: 3D…
- PDB
- 5XRF
- Type
- protein
- Length
- 236 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Snake venom serine protease da-36
- UniProt
- J7LCB0
- Ligands
- NAG, BMA, FUC, MAN
- Pockets
- 1 · best druggability 0.36
Structure
x-ray diffraction · 1 distinct chain · 8% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Snake venom serine protease da-36 | protein | 236 | 8% helix, 34% strand | J7LCB0 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A
- BMA · beta-D-mannopyranose · sugar · 2 copies
- FUC · alpha-L-fucopyranose · sugar · 2 copies · chains A
- MAN · alpha-D-mannopyranose · sugar · chains A
- PEG · Di(hydroxyethyl)ether · additive · chains A
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 | 55 | 0.36 | 0.79 | 18 | empty |
Modifications
Observed in the structure: 6 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 5XRF · Crystal structure of Da-36, a thrombin-like enzyme from Deinagkistrodon acutus · the same entry in another collection · chain A against A, 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 J7LCB0
- Elsewhere: RCSB PDB 5XRF · PDBe 5XRF · UniProt J7LCB0
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