Research workbench
Crystal structure of aplysia cyclase complexed with substrate ngd and product cgdpr
Analyse Crystal structure of aplysia cyclase complexed with substrate ngd and product… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3ZWN
- Type
- protein
- Length
- 505 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ADP-ribosyl cyclase
- EC
- 3.2.2.5
- UniProt
- P29241
- Ligands
- CGR, NGD
- Pockets
- 5 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ADP-ribosyl cyclase (EC 3.2.2.5) | protein | 253 | 43% helix, 14% strand | P29241 |
| B | ADP-ribosyl cyclase (EC 3.2.2.5) | protein | 252 | 40% helix, 13% strand | P29241 |
Ligands and binding sites
- CGR · Cyclic guanosine diphosphate-ribose · ligand · chains A
- NGD · 3-(aminocarbonyl)-1-[(2R,3R,4S,5R)-5-({[(S)-{[(S)-{[(2R,3S,4R,5R)-5-(2-amino-6-oxo-1,6-dihydro-9H-purin-9-yl)-3,4-dihyd roxytetrahydrofuran-2-yl]methoxy}(hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]oxy}methyl)-3,4-dihydroxytetrahydrofuran-2- yl]pyridinium · ligand · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 790 | 0.74 | 0.79 | 63 | empty |
| 2 | 363 | 0.70 | 0.82 | 51 | NGD |
| 3 | 148 | 0.56 | 0.81 | 19 | empty |
| 4 | 134 | 0.46 | 0.77 | 26 | CGR |
| 5 | 57 | 0.36 | 0.78 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 1488 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide (disulfide).
Compared structures
- 3ZWN · Crystal structure of Aplysia cyclase complexed with substrate NGD and product cGDPR · the same entry in another collection · chain A against A, TM-score 1.00
- P29241 · AlphaFold monomer V2.0 prediction for ADP-ribosyl CYCLASE/CYCLIC ADP- ribose hydrolase… · a predicted model of the same protein · chain B 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 P29241
- Elsewhere: RCSB PDB 3ZWN · PDBe 3ZWN · UniProt P29241
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