MolNFT v1 · #64918 · protein
Structural insights into the catalytic mechanism of CD38: evidence for a conformationally flexible covalent enzyme-substrate complex.
3GHH · Ecto-NAD+ glycohydrolase (CD38 molecule): “Structural insights into the catalytic mechanism of CD38: evidence for a conformationally flexible covalent…”. X-ray diffraction, 3 ligands (2NF, NAG, SO4), 5 pockets (best druggability…
- PDB
- 3GHH
- Type
- protein
- Length
- 475 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
- 2NF, NAG, SO4
- Pockets
- 5 · best druggability 0.70
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ecto-NAD+ glycohydrolase (CD38 molecule) (EC 3.2.2.5) | protein | 238 | 42% helix, 15% strand | Q9TTF5 |
| B | Ecto-NAD+ glycohydrolase (CD38 molecule) (EC 3.2.2.5) | protein | 237 | 41% helix, 13% strand | Q9TTF5 |
Ligands and binding sites
- 2NF · [[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-dihydroxyoxolan-2-yl]methoxy-hydroxyphosphoryl] [(2R,3S,4R,5R)-5-(3-carbamoylpyridin-1-ium-1yl)- 3-fluoro-,4- hydroxyoxolan-2-yl]methyl phosphate · ligand · chains B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, B
- SO4 · Sulfate ion · ion · 5 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 | 255 | 0.70 | 0.85 | 30 | SO4 |
| 2 | 280 | 0.68 | 0.84 | 42 | SO4 |
| 3 | 331 | 0.62 | 0.78 | 39 | 2NF |
| 4 | 263 | 0.55 | 0.76 | 30 | empty |
| 5 | 69 | 0.28 | 0.73 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 1027 Ų buried · 23 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 3GHH · 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 3GHH · PDBe 3GHH · UniProt Q9TTF5
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