Research workbench
Crystal structure of ADP-ribosyl cyclase complexed with ara-2'F-ADP- ribose at 2.3 ångström
Analyse Crystal structure of ADP-ribosyl cyclase complexed with ara-2'F-ADP- ribose at… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3ZWV
- Type
- protein
- Length
- 2,010 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
- AVU
- Pockets
- 20 · best druggability 0.77
Structure
x-ray diffraction · 3 distinct chains · 41% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ADP-ribosyl cyclase (EC 3.2.2.5) | protein | 252 | 42% helix, 12% strand | P29241 |
| B, C, E, F, G, H | ADP-ribosyl cyclase (EC 3.2.2.5) | protein | 251 | 41% helix, 12% strand | P29241 |
| D | ADP-ribosyl cyclase (EC 3.2.2.5) | protein | 252 | 41% helix, 12% strand | P29241 |
Ligands and binding sites
- AVU · [(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl [(2R,3R,4R)-4-fluoro-3-hydroxytetrahydrofuran-2-yl]methyl dihydrogen diphosphate · ligand · 8 copies · chains A, B, C, D, E, F, G, H
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 | 750 | 0.77 | 0.82 | 60 | empty |
| 2 | 975 | 0.77 | 0.79 | 112 | AVU |
| 3 | 1042 | 0.77 | 0.79 | 78 | empty |
| 4 | 1021 | 0.76 | 0.78 | 77 | empty |
| 5 | 879 | 0.74 | 0.78 | 65 | empty |
Interfaces
9 interfaces between chains.
- E–F · 1564 Ų buried · 20 hydrogen bonds · protein-protein
- G–H · 1558 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 1465 Ų buried · 15 hydrogen bonds · protein-protein
- C–D · 1450 Ų buried · 16 hydrogen bonds · protein-protein
- D–E · 867 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 40 disulfide, 8 covalent (disulfide, covalent ligand).
Compared structures
- 3ZWV · Crystal structure of ADP-ribosyl cyclase complexed with ara-2'F-ADP- ribose at 2.3… · 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 A against A, TM-score 0.99
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 3ZWV · PDBe 3ZWV · UniProt P29241
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