MolNFT v1 · #175763 · protein
Crystal structure of taiwan cobra 5'-nucleotidase
7D0V · Snake venom 5'-nucleotidase: “Crystal structure of taiwan cobra 5'-nucleotidase”. X-ray diffraction, 5 ligands (NAG, BMA, FUC), 11 pockets (best druggability 0.87). MolNFT v1 #175763 on GenesisL1: 3D structure, binding sites and…
- PDB
- 7D0V
- Type
- protein
- Length
- 1,052 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Snake venom 5'-nucleotidase
- EC
- 3.1.3.5
- Ligands
- NAG, BMA, FUC, ZN, CA
- Pockets
- 11 · best druggability 0.87
Structure
x-ray diffraction · 1 distinct chain · 30% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Snake venom 5'-nucleotidase (EC 3.1.3.5) | protein | 526 | 30% helix, 27% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains A, B
- BMA · beta-D-mannopyranose · sugar · 2 copies
- FUC · alpha-L-fucopyranose · sugar · chains A
- ZN · Zinc ion · metal · 4 copies · chains A, B
- CA · Calcium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 509 | 0.87 | 0.93 | 51 | empty |
| 2 | 668 | 0.69 | 0.77 | 76 | empty |
| 3 | 609 | 0.67 | 0.76 | 65 | empty |
| 4 | 523 | 0.66 | 0.78 | 56 | empty |
| 5 | 514 | 0.63 | 0.76 | 59 | empty |
Interfaces
1 interface between chains.
- A–B · 1419 Ų buried · 22 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
- 7D0V · Crystal structure of Taiwan cobra 5'-nucleotidase · 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
- Elsewhere: RCSB PDB 7D0V · PDBe 7D0V
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