Research workbench
Crystal structure of wild type human CD38 in complex with naadp and adprp
Analyse Crystal structure of wild type human CD38 in complex with naadp and adprp in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4F46
- Type
- protein
- Length
- 500 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
- DVN, DN4
- Pockets
- 6 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ADP-ribosyl cyclase 1 (EC 3.2.2.5) | protein | 248 | 44% helix, 15% strand | P28907 |
| B | ADP-ribosyl cyclase 1 (EC 3.2.2.5) | protein | 252 | 43% helix, 14% strand | P28907 |
Ligands and binding sites
- DVN · [[(2R,3R,4R,5R)-5-(6-aminopurin-9-yl)-3-oxidanyl-4-phosphonooxy-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2R,3S,4R,5S)-3,4,5-tris(oxidanyl)oxolan-2-yl]methyl hydrogen phosphate · ligand · chains A
- DN4 · [[(2R,3R,4R,5R)-5-(6-aminopurin-9-yl)-3-oxidanyl-4-phosphonooxy-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2R,3S,4R,5R)-5-(3-carboxypyridin-1-ium-1-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl phosphate · ligand · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 714 | 0.75 | 0.80 | 85 | DN4 |
| 2 | 344 | 0.64 | 0.79 | 43 | DVN |
| 3 | 95 | 0.55 | 0.84 | 14 | empty |
| 4 | 86 | 0.53 | 0.84 | 16 | empty |
| 5 | 76 | 0.37 | 0.77 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 597 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 11 disulfide (disulfide).
Compared structures
- 4F46 · Crystal structure of wild type human CD38 in complex with NAADP and ADPRP · 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 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 P28907
- Elsewhere: RCSB PDB 4F46 · PDBe 4F46 · UniProt P28907
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