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Crystal structure of ADP ribosyl cyclase complexed with substrate NAD and product cadpr
Analyse Crystal structure of ADP ribosyl cyclase complexed with substrate NAD and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3ZWM
- Type
- protein
- Length
- 2,015 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ADP-ribosyl cylcase
- EC
- 3.2.2.5
- UniProt
- P29241
- Ligands
- NAD, CXR
- Pockets
- 20 · best druggability 0.77
Structure
x-ray diffraction · 5 distinct chains · 41% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ADP-ribosyl cylcase (EC 3.2.2.5) | protein | 252 | 39% helix, 13% strand | P29241 |
| B | ADP-ribosyl cylcase (EC 3.2.2.5) | protein | 251 | 41% helix, 13% strand | P29241 |
| C, E, F, H | ADP-ribosyl cylcase (EC 3.2.2.5) | protein | 253 | 42% helix, 14% strand | P29241 |
| D | ADP-ribosyl cylcase (EC 3.2.2.5) | protein | 250 | 42% helix, 13% strand | P29241 |
| G | ADP-ribosyl cylcase (EC 3.2.2.5) | protein | 250 | 41% helix, 12% strand | P29241 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 6 copies · chains A, B, C, D, E, G
- CXR · Cyclic adenosine diphosphate-ribose · ligand · 2 copies · chains F, 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 | 555 | 0.77 | 0.84 | 60 | empty |
| 2 | 1004 | 0.77 | 0.79 | 75 | empty |
| 3 | 971 | 0.77 | 0.80 | 68 | empty |
| 4 | 959 | 0.76 | 0.79 | 67 | empty |
| 5 | 386 | 0.75 | 0.85 | 53 | CXR |
Interfaces
10 interfaces between chains.
- E–F · 1487 Ų buried · 12 hydrogen bonds · protein-protein
- G–H · 1481 Ų buried · 20 hydrogen bonds · protein-protein
- A–B · 1380 Ų buried · 14 hydrogen bonds · protein-protein
- C–D · 1320 Ų buried · 20 hydrogen bonds · protein-protein
- D–E · 934 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 38 disulfide (disulfide).
Compared structures
- 3ZWM · Crystal structure of ADP ribosyl cyclase complexed with substrate NAD and product cADPR · 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 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 3ZWM · PDBe 3ZWM · UniProt P29241
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