MolNFT v1 · #120674 · protein
Crystal structure of 5'-nucleotidase from venom of naja atra
5H7W · Venom 5'-nucleotidase: “Crystal structure of 5'-nucleotidase from venom of naja atra”. X-ray diffraction, 4 ligands (NAG, BMA, ZN), 10 pockets (best druggability 0.85). MolNFT v1 #120674 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5H7W
- Type
- protein
- Length
- 1,057 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Venom 5'-nucleotidase
- Ligands
- NAG, BMA, ZN, CA
- Pockets
- 10 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 31% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Venom 5'-nucleotidase | protein | 528 | 31% helix, 26% strand | — |
| B | Venom 5'-nucleotidase | protein | 529 | 30% helix, 26% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 5 copies · chains A, B
- BMA · beta-D-mannopyranose · sugar · 2 copies
- 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
10 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 567 | 0.85 | 0.90 | 59 | empty |
| 2 | 667 | 0.68 | 0.77 | 77 | empty |
| 3 | 698 | 0.68 | 0.76 | 74 | empty |
| 4 | 553 | 0.68 | 0.78 | 66 | empty |
| 5 | 542 | 0.65 | 0.76 | 54 | empty |
Interfaces
1 interface between chains.
- A–B · 1474 Ų buried · 22 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 5H7W · Crystal structure of 5'-nucleotidase from venom of Naja atra · 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 5H7W · PDBe 5H7W
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