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Crystal structure of human CD38: cyclic-ADP-ribosyl SYNTHETASE/NAD+ glycohydrolase
Analyse Crystal structure of human CD38: cyclic-ADP-ribosyl SYNTHETASE/NAD+… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1ZVM
- Type
- protein
- Length
- 1,009 residues
- Chains
- 4
- 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
- SO4
- Pockets
- 15 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D | ADP-ribosyl cyclase 1 (EC 3.2.2.5) | protein | 252 | 42% helix, 14% strand | P28907 |
| C | ADP-ribosyl cyclase 1 (EC 3.2.2.5) | protein | 253 | 44% helix, 14% strand | P28907 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 8 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 889 | 0.73 | 0.77 | 85 | SO4 |
| 2 | 388 | 0.72 | 0.83 | 49 | empty |
| 3 | 357 | 0.59 | 0.76 | 39 | SO4 |
| 4 | 315 | 0.57 | 0.76 | 39 | SO4 |
| 5 | 291 | 0.55 | 0.76 | 39 | SO4 |
Interfaces
3 interfaces between chains.
- A–D · 540 Ų buried · 3 hydrogen bonds · protein-protein
- A–B · 482 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 452 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 24 disulfide (disulfide).
Compared structures
- 1ZVM · Crystal structure of human CD38: cyclic-ADP-ribosyl synthetase/NAD+ glycohydrolase · the same entry in another collection · chain D against D, 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 0.98
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 1ZVM · PDBe 1ZVM · UniProt P28907
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