Research workbench
Structural insights into the catalytic mechanism of CD38: evidence for a conformationally flexible covalent enzyme-substrate complex.
Analyse Structural insights into the catalytic mechanism of CD38: evidence for a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3GH3
- Type
- protein
- Length
- 482 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ecto-NAD+ glycohydrolase (CD38 molecule)
- EC
- 3.2.2.5
- UniProt
- Q9TTF5
- Ligands
- NAG, SO4
- Pockets
- 5 · best druggability 0.70
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ecto-NAD+ glycohydrolase (CD38 molecule) (EC 3.2.2.5) | protein | 241 | 43% helix, 14% strand | Q9TTF5 |
| B | Ecto-NAD+ glycohydrolase (CD38 molecule) (EC 3.2.2.5) | protein | 241 | 41% helix, 14% strand | Q9TTF5 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, B
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
- CAC · Cacodylate ion · additive · chains 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, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 381 | 0.70 | 0.82 | 40 | empty |
| 2 | 411 | 0.68 | 0.81 | 49 | SO4 |
| 3 | 320 | 0.59 | 0.77 | 25 | empty |
| 4 | 246 | 0.54 | 0.77 | 29 | CAC |
| 5 | 58 | 0.54 | 0.88 | 12 | empty |
Interfaces
1 interface between chains.
- A–B · 920 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 3GH3 · Structural insights into the catalytic mechanism of CD38: Evidence for a conformationally… · the same entry in another collection · chain A against A, TM-score 1.00
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 Q9TTF5
- Elsewhere: RCSB PDB 3GH3 · PDBe 3GH3 · UniProt Q9TTF5
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