Research workbench
Crystal structure of ADP ribosyl cyclase complexed with reaction intermediate
Analyse Crystal structure of ADP ribosyl cyclase complexed with reaction intermediate in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3ZWO
- Type
- protein
- Length
- 2,011 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ADP-ribosyl cyclase
- EC
- 3.2.2.5
- UniProt
- P29241
- Ligands
- G2Q, NGD
- Pockets
- 20 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, G | ADP-ribosyl cyclase (EC 3.2.2.5) | protein | 252 | 40% helix, 13% strand | P29241 |
| B, D, E, F, H | ADP-ribosyl cyclase (EC 3.2.2.5) | protein | 251 | 41% helix, 13% strand | P29241 |
Ligands and binding sites
- G2Q · Guanosine diphosphate ribose · ligand · 6 copies · chains A, B, C, E, G, H
- 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 F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 977 | 0.78 | 0.80 | 71 | empty |
| 2 | 925 | 0.76 | 0.79 | 60 | empty |
| 3 | 933 | 0.76 | 0.79 | 63 | empty |
| 4 | 906 | 0.76 | 0.79 | 60 | empty |
| 5 | 871 | 0.73 | 0.77 | 103 | G2Q |
Interfaces
8 interfaces between chains.
- B–G · 1539 Ų buried · 17 hydrogen bonds · protein-protein
- E–H · 1533 Ų buried · 15 hydrogen bonds · protein-protein
- C–F · 1502 Ų buried · 17 hydrogen bonds · protein-protein
- A–D · 1492 Ų buried · 18 hydrogen bonds · protein-protein
- A–E · 949 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 40 disulfide (disulfide).
Compared structures
- 3ZWO · Crystal structure of ADP ribosyl cyclase complexed with reaction intermediate · the same entry in another collection · chain H against H, 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 3ZWO · PDBe 3ZWO · UniProt P29241
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.