Research workbench
Crystal structure of human CD38 in complex with hydrolysed compound JMS713
Analyse Crystal structure of human CD38 in complex with hydrolysed compound JMS713 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4TMF
- Type
- protein
- Length
- 486 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ADP-ribosyl CYCLASE/CYCLIC ADP-ribose hydrolase 1
- EC
- 3.2.2.6, 2.4.99.20
- UniProt
- P28907
- Ligands
- JS2
- Pockets
- 5 · best druggability 0.70
Structure
x-ray diffraction · 2 distinct chains · 44% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ADP-ribosyl CYCLASE/CYCLIC ADP-ribose hydrolase 1 (EC 3.2.2.6, 2.4.99.20) | protein | 244 | 45% helix, 15% strand | P28907 |
| B | ADP-ribosyl CYCLASE/CYCLIC ADP-ribose hydrolase 1 (EC 3.2.2.6, 2.4.99.20) | protein | 242 | 44% helix, 15% strand | P28907 |
Ligands and binding sites
- JS2 · 5-O-[(R)-{[(S)-[4-(8-amino-6-oxo-1,6-dihydro-9H-purin-9-yl)butoxy](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]-alpha-D- ribofuranose · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 645 | 0.70 | 0.78 | 63 | JS2 |
| 2 | 626 | 0.67 | 0.77 | 64 | JS2 |
| 3 | 68 | 0.57 | 0.88 | 15 | empty |
| 4 | 63 | 0.52 | 0.86 | 14 | empty |
| 5 | 84 | 0.33 | 0.74 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 569 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 11 disulfide (disulfide).
Compared structures
- 4TMF · Crystal structure of human CD38 in complex with hydrolysed compound JMS713 · 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 4TMF · PDBe 4TMF · UniProt P28907
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