Research workbench
Crystal structure of snake venom phosphodiesterase (pde) from taiwan cobra (naja atra atra) in complex with AMP
Analyse Crystal structure of snake venom phosphodiesterase (pde) from taiwan cobra… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.