MolNFT v1 · #46419 · protein
Structural basis for formation and hydrolysis of calcium messenger cyclic ADP-ribose by human CD38
2O3U · ADP-ribosyl cyclase 1: “Structural basis for formation and hydrolysis of calcium messenger cyclic ADP-ribose by human CD38”. X-ray diffraction, 1 ligand (NGD), 7 pockets (best druggability 0.74). MolNFT v1 #46419 on GenesisL1: 3D…
- PDB
- 2O3U
- Type
- protein
- Length
- 504 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ADP-ribosyl cyclase 1
- EC
- 3.2.2.5
- UniProt
- P28907
- Ligands
- NGD
- Pockets
- 7 · best druggability 0.74
Structure
x-ray diffraction · 1 distinct chain · 42% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | ADP-ribosyl cyclase 1 (EC 3.2.2.5) | protein | 252 | 42% helix, 13% strand | P28907 |
Ligands and binding sites
- NGD · 3-(aminocarbonyl)-1-[(2R,3R,4S,5R)-5-({[(S)-{[(S)-{[(2R,3S,4R,5R)-5-(2-amino-6-oxo-1,6-dihydro-9H-purin-9-yl)-3,4-dihyd roxytetrahydrofuran-2-yl]methoxy}(hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]oxy}methyl)-3,4-dihydroxytetrahydrofuran-2- yl]pyridinium · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 713 | 0.74 | 0.80 | 69 | NGD |
| 2 | 329 | 0.62 | 0.78 | 40 | NGD |
| 3 | 105 | 0.57 | 0.85 | 18 | empty |
| 4 | 109 | 0.54 | 0.83 | 16 | empty |
| 5 | 78 | 0.41 | 0.79 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 481 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide (disulfide).
Compared structures
- 2O3U · Structural Basis for Formation and Hydrolysis of Calcium Messenger Cyclic ADP-ribose by… · the same entry in another collection · chain A against A, TM-score 1.00
- P28907 · AlphaFold monomer V2.0 prediction for ADP-ribosyl CYCLASE/CYCLIC ADP- ribose hydrolase 1… · a predicted model of the same protein · chain B 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 P28907
- Elsewhere: RCSB PDB 2O3U · PDBe 2O3U · UniProt P28907
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