MolNFT v1 · #55224 · protein
Cpoga D298N in complex with P53-derived O-glcnac peptide
2YDR · O-glcnacase nagj: “Cpoga D298N in complex with P53-derived O-glcnac peptide”. X-ray diffraction, 2 ligands (NAG, CD), 7 pockets (best druggability 0.41). MolNFT v1 #55224 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 2YDR
- Type
- protein
- Length
- 587 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- O-glcnacase nagj; Cellular tumor antigen P53
- EC
- 3.2.1.52
- UniProt
- Q0TR53, P04637
- Ligands
- NAG, CD
- Pockets
- 7 · best druggability 0.41
Structure
x-ray diffraction · 2 distinct chains · 46% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | O-glcnacase nagj (EC 3.2.1.52) | protein | 579 | 47% helix, 16% strand | Q0TR53 |
| P | Cellular tumor antigen P53 | protein | 8 | 0% helix, 0% strand | P04637 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains A, P
- CD · Cadmium ion · metal · 18 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 74 | 0.41 | 0.80 | 19 | CD |
| 2 | 133 | 0.41 | 0.74 | 15 | empty |
| 3 | 78 | 0.41 | 0.78 | 18 | empty |
| 4 | 93 | 0.39 | 0.77 | 16 | empty |
| 5 | 85 | 0.37 | 0.76 | 15 | empty |
Interfaces
1 interface between chains.
- A–P · 369 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 1 glycan (O-glycosylation).
Compared structures
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 Q0TR53
- Every structure of UniProt P04637
- Elsewhere: RCSB PDB 2YDR · PDBe 2YDR · UniProt Q0TR53 · UniProt P04637
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