Research workbench
Crystal structure of ADP ribosyl cyclase complexed with a substrate analog and a product nicotinamide
Analyse Crystal structure of ADP ribosyl cyclase complexed with a substrate analog and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3I9J
- Type
- protein
- Length
- 502 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
- NFD, AVV, NCA
- Pockets
- 4 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 41% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | ADP-ribosyl cyclase (EC 3.2.2.5) | protein | 251 | 41% helix, 13% strand | P29241 |
Ligands and binding sites
- NFD · Nicotinamide 2-fluoro-adenine dinucleotide · ligand · chains A
- AVV · [(2R,3S,4R,5R)-5-(6-amino-2-fluoro-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl [(2R,3S,4S)-3,4-dihydroxytetrahydrofuran-2-yl]methyl dihydrogen diphosphate · ligand · chains B
- NCA · Nicotinamide · ligand · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1113 | 0.76 | 0.78 | 82 | empty |
| 2 | 314 | 0.60 | 0.78 | 44 | AVV, NCA |
| 3 | 272 | 0.60 | 0.78 | 37 | NFD |
| 4 | 54 | 0.25 | 0.73 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 1516 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide (disulfide).
Compared structures
- 3I9J · Crystal structure of ADP ribosyl cyclase complexed with a substrate analog and a product… · the same entry in another collection · chain B against B, 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 3I9J · PDBe 3I9J · UniProt P29241
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