MolNFT v1 · #120395 · protein
Crystal structure of snake venom phosphodiesterase (pde) from taiwan cobra (naja atra atra) in complex with AMP
5GZ5: “Crystal structure of snake venom phosphodiesterase (pde) from taiwan cobra (naja atra atra) in complex with…”. X-ray diffraction, 7 ligands (AMP, NAG, FUC), 12 pockets (best druggability 0.64). MolNFT v1 #120395 on GenesisL1: 3D…
- PDB
- 5GZ5
- Type
- protein
- Length
- 777 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Snake venom phosphodiesterase (pde)
- Ligands
- AMP, NAG, FUC, BMA, MAN, ZN, CA
- Pockets
- 12 · best druggability 0.64
Structure
x-ray diffraction · 1 distinct chain · 28% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Snake venom phosphodiesterase (pde) | protein | 777 | 28% helix, 19% strand | — |
Ligands and binding sites
- AMP · Adenosine monophosphate · ligand · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains A
- FUC · alpha-L-fucopyranose · sugar · 2 copies · chains A
- BMA · beta-D-mannopyranose · sugar
- MAN · alpha-D-mannopyranose · sugar
- ZN · Zinc ion · metal · 2 copies · chains A
- CA · Calcium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 326 | 0.64 | 0.80 | 48 | empty |
| 2 | 241 | 0.60 | 0.80 | 28 | empty |
| 3 | 342 | 0.59 | 0.77 | 43 | AMP |
| 4 | 248 | 0.56 | 0.78 | 41 | empty |
| 5 | 290 | 0.55 | 0.76 | 43 | NAG |
Modifications
Observed in the structure: 12 disulfide, 6 glycan (disulfide, N-glycosylation).
Compared structures
- 5GZ5 · Crystal structure of snake venom phosphodiesterase (PDE) from Taiwan cobra (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 5GZ5 · PDBe 5GZ5
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