MolNFT v1 · #55223 · protein
Cpoga D298N in complex with hoga-derived O-glcnac peptide
2YDQ · O-glcnacase nagj: “Cpoga D298N in complex with hoga-derived O-glcnac peptide”. X-ray diffraction, 2 ligands (NAG, CD), 5 pockets (best druggability 0.40). MolNFT v1 #55223 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 2YDQ
- Type
- protein
- Length
- 585 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- O-glcnacase nagj; Bifunctional protein ncoat
- EC
- 3.2.1.52, 3.2.1.169
- UniProt
- Q0TR53, O60502
- Ligands
- NAG, CD
- Pockets
- 5 · best druggability 0.40
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 | 46% helix, 15% strand | Q0TR53 |
| T | Bifunctional protein ncoat (EC 3.2.1.169) | protein | 6 | 0% helix, 0% strand | O60502 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains A, T
- CD · Cadmium ion · metal · 19 copies · chains A, T
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 130 | 0.40 | 0.74 | 21 | empty |
| 2 | 61 | 0.37 | 0.79 | 15 | empty |
| 3 | 61 | 0.37 | 0.79 | 18 | empty |
| 4 | 82 | 0.36 | 0.76 | 16 | empty |
| 5 | 73 | 0.33 | 0.75 | 14 | CD |
Interfaces
1 interface between chains.
- A–T · 295 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 glycan (O-glycosylation).
Compared structures
- 2YDQ · CpOGA D298N in complex with hOGA-derived O-GlcNAc peptide · the same entry in another collection · chain T against T, TM-score 1.00
- Q0TR53 · AlphaFold monomer V2.0 prediction for O-glcnacase nagj (Q0TR53) · a predicted model of the same protein · chain A against A, TM-score 0.99
- O60502 · AlphaFold monomer V2.0 prediction for protein O-glcnacase (O60502) · a predicted model of the same protein · chain T against A, TM-score 0.41
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 O60502
- Elsewhere: RCSB PDB 2YDQ · PDBe 2YDQ · UniProt Q0TR53 · UniProt O60502
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