Research workbench
Crystal structure of snake venom phosphodiesterase (pde) from taiwan cobra (naja atra atra)
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
- 5GZ4
- Type
- protein
- Length
- 804 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Snake venom phosphodiesterase (pde)
- Ligands
- NAG, MAN, FUC, BMA, ZN, CA
- Pockets
- 14 · best druggability 0.61
Structure
x-ray diffraction · 1 distinct chain · 27% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Snake venom phosphodiesterase (pde) | protein | 804 | 27% helix, 18% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains A
- MAN · alpha-D-mannopyranose · sugar · 2 copies · chains A
- FUC · alpha-L-fucopyranose · sugar · chains A
- BMA · beta-D-mannopyranose · sugar
- ZN · Zinc ion · metal · 2 copies · chains A
- CA · Calcium ion · metal · chains A
- EDO · 1,2-ethanediol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 343 | 0.61 | 0.78 | 40 | empty |
| 2 | 288 | 0.59 | 0.78 | 40 | NAG |
| 3 | 340 | 0.57 | 0.76 | 38 | empty |
| 4 | 198 | 0.56 | 0.80 | 27 | empty |
| 5 | 129 | 0.51 | 0.80 | 23 | empty |
Modifications
Observed in the structure: 16 disulfide, 6 glycan (disulfide, N-glycosylation).
Compared structures
- 5GZ4 · 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 5GZ4 · PDBe 5GZ4
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