Research workbench
Crystal structure of human CD38 extracellular domain, ara-F-ribose-5'- PHOSPHATE/NICOTINAMIDE complex
Analyse Crystal structure of human CD38 extracellular domain, ara-F-ribose-5'… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3DZG
- 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
- RF5, NCA
- Pockets
- 5 · best druggability 0.70
Structure
x-ray diffraction · 1 distinct chain · 44% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | ADP-ribosyl cyclase 1 (EC 3.2.2.5) | protein | 252 | 44% helix, 16% strand | P28907 |
Ligands and binding sites
- RF5 · 2-deoxy-2-fluoro-5-O-phosphono-alpha-D-arabinofuranose · ligand · 2 copies · chains A, B
- NCA · Nicotinamide · 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 | 679 | 0.70 | 0.78 | 71 | RF5, NCA |
| 2 | 639 | 0.68 | 0.77 | 75 | RF5, NCA |
| 3 | 72 | 0.57 | 0.88 | 19 | empty |
| 4 | 107 | 0.53 | 0.82 | 16 | empty |
| 5 | 102 | 0.37 | 0.74 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 600 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide, 2 covalent (disulfide, covalent ligand).
Compared structures
- 3DZG · Crystal structure of human CD38 extracellular domain… · 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 0.98
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 3DZG · PDBe 3DZG · UniProt P28907
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