Research workbench
Aplysia ADP ribosyl cyclase with bound nicotinamide and R5P
Analyse Aplysia ADP ribosyl cyclase with bound nicotinamide and R5P in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1R15
- Type
- protein
- Length
- 2,008 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
- NCA, N
- Pockets
- 17 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 41% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H | ADP-ribosyl cyclase (EC 3.2.2.5) | protein | 251 | 41% helix, 13% strand | P29241 |
Ligands and binding sites
- NCA · Nicotinamide · ligand · 16 copies · chains A, B, C, D, E, F, G, H
- N · Any 5'-monophosphate nucleotide · 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
17 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1072 | 0.79 | 0.81 | 103 | empty |
| 2 | 582 | 0.78 | 0.84 | 57 | empty |
| 3 | 977 | 0.77 | 0.79 | 76 | empty |
| 4 | 966 | 0.76 | 0.79 | 79 | empty |
| 5 | 193 | 0.70 | 0.87 | 24 | NCA |
Interfaces
10 interfaces between chains.
- G–H · 1540 Ų buried · 19 hydrogen bonds · protein-protein
- E–F · 1538 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 1527 Ų buried · 18 hydrogen bonds · protein-protein
- C–D · 1521 Ų buried · 16 hydrogen bonds · protein-protein
- D–G · 857 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 40 disulfide, 8 covalent (disulfide, covalent ligand).
Compared structures
- 1R15 · Aplysia ADP ribosyl cyclase with bound nicotinamide and R5P · 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 1R15 · PDBe 1R15 · UniProt P29241
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