Research workbench
Crystal structure of human CD38 complexed with an analog ara-2'F-adpr
Analyse Crystal structure of human CD38 complexed with an analog ara-2'F-adpr in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3I9M
- 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
- AVU
- Pockets
- 6 · best druggability 0.71
Structure
x-ray diffraction · 1 distinct chain · 44% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | ADP-ribosyl cyclase 1 (EC 3.2.2.5) | protein | 252 | 44% helix, 14% strand | P28907 |
Ligands and binding sites
- AVU · [(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl [(2R,3R,4R)-4-fluoro-3-hydroxytetrahydrofuran-2-yl]methyl dihydrogen diphosphate · ligand · 2 copies · chains A, 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 | 629 | 0.71 | 0.79 | 64 | AVU |
| 2 | 516 | 0.66 | 0.77 | 51 | AVU |
| 3 | 68 | 0.55 | 0.87 | 17 | empty |
| 4 | 104 | 0.52 | 0.82 | 16 | empty |
| 5 | 98 | 0.38 | 0.76 | 26 | empty |
Interfaces
1 interface between chains.
- A–B · 590 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide, 2 covalent (disulfide, covalent ligand).
Compared structures
- 3I9M · Crystal structure of human CD38 complexed with an analog ara-2'F-ADPR · the same entry in another collection · chain B against B, 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 3I9M · PDBe 3I9M · UniProt P28907
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