MolNFT v1 · #19995 · protein
Aplysia ADP ribosyl cyclase with bound pyridylcarbinol and R5P
1R16 · ADP-ribosyl cyclase: “Aplysia ADP ribosyl cyclase with bound pyridylcarbinol and R5P”. X-ray diffraction, 2 ligands (N, PYF), 4 pockets (best druggability 0.76). MolNFT v1 #19995 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 1R16
- 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
- N, PYF
- Pockets
- 4 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 43% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | ADP-ribosyl cyclase (EC 3.2.2.5) | protein | 251 | 43% helix, 13% strand | P29241 |
Ligands and binding sites
- N · Any 5'-monophosphate nucleotide · ligand · 2 copies · chains A, B
- PYF · 3-pyridinylcarbinol · ligand · 2 copies · chains A, 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 | 898 | 0.76 | 0.79 | 70 | empty |
| 2 | 299 | 0.62 | 0.79 | 44 | N, PYF |
| 3 | 288 | 0.61 | 0.79 | 47 | N, PYF |
| 4 | 51 | 0.24 | 0.72 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 1478 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide, 2 covalent (disulfide, covalent ligand).
Compared structures
- 1R16 · Aplysia ADP ribosyl cyclase with bound pyridylcarbinol and R5P · the same entry in another collection · chain A against A, 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 1R16 · PDBe 1R16 · UniProt P29241
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