MolNFT v1 · #74745 · protein
Structural insights into the catalytic mechanism of CD38: evidence for a conformationally flexible covalent enzyme-substrate complex
3P5S · CD38 molecule: “Structural insights into the catalytic mechanism of CD38: evidence for a conformationally flexible covalent…”. X-ray diffraction, 3 ligands (AVU, NAG, SO4), 5 pockets (best druggability 0.68). MolNFT v1 #74745 on…
- PDB
- 3P5S
- Type
- protein
- Length
- 473 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- CD38 molecule
- EC
- 3.2.2.5
- UniProt
- Q9TTF5
- Ligands
- AVU, NAG, SO4
- Pockets
- 5 · best druggability 0.68
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | CD38 molecule (EC 3.2.2.5) | protein | 238 | 42% helix, 14% strand | Q9TTF5 |
| B | CD38 molecule (EC 3.2.2.5) | protein | 235 | 41% helix, 12% strand | Q9TTF5 |
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
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 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 | 261 | 0.68 | 0.84 | 41 | empty |
| 2 | 188 | 0.61 | 0.83 | 41 | SO4 |
| 3 | 296 | 0.58 | 0.77 | 32 | AVU |
| 4 | 201 | 0.53 | 0.77 | 23 | AVU |
| 5 | 59 | 0.29 | 0.74 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 1050 Ų buried · 22 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide (disulfide).
Compared structures
- 3P5S · 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 3P5S · PDBe 3P5S · UniProt Q9TTF5
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