Research workbench
Crystal structure of snake venom phosphodiesterase (pde) from taiwan cobra (naja atra atra) in complex with isorhamnetin and citrate
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
- 7CBA
- Type
- protein
- Length
- 1,536 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Venom phosphodiesterase
- EC
- 3.6.1.-
- UniProt
- A0A2D0TC04
- Ligands
- IRH, NAG, BMA, ZN, CA
- Pockets
- 20 · best druggability 0.63
Structure
x-ray diffraction · 2 distinct chains · 29% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Venom phosphodiesterase (EC 3.6.1.-) | protein | 768 | 29% helix, 19% strand | A0A2D0TC04 |
| B | Venom phosphodiesterase (EC 3.6.1.-) | protein | 768 | 30% helix, 19% strand | A0A2D0TC04 |
Ligands and binding sites
- IRH · isorhamnetin · ligand · 2 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 11 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
- CIT · Citric acid · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 363 | 0.63 | 0.79 | 53 | empty |
| 2 | 391 | 0.60 | 0.76 | 40 | ZN, IRH, CIT |
| 3 | 270 | 0.59 | 0.79 | 33 | empty |
| 4 | 229 | 0.56 | 0.78 | 35 | empty |
| 5 | 264 | 0.54 | 0.76 | 41 | NAG |
Interfaces
1 interface between chains.
- A–B · 718 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 24 disulfide, 9 glycan (disulfide, N-glycosylation).
Compared structures
- 7CBA · 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
- Every structure of UniProt A0A2D0TC04
- Elsewhere: RCSB PDB 7CBA · PDBe 7CBA · UniProt A0A2D0TC04
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