Research workbench
Cpoga D298N in complex with TAB1-derived O-glcnac peptide
Analyse Cpoga D298N in complex with TAB1-derived O-glcnac peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2YDS
- Type
- protein
- Length
- 584 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- O-glcnacase nagj; TGF-beta-activated kinase 1 and MAP3K7-binding protein 1
- EC
- 3.2.1.169
- UniProt
- Q0TR53, Q15750
- Ligands
- NAG, CD
- Pockets
- 6 · best druggability 0.42
Structure
x-ray diffraction · 2 distinct chains · 46% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | O-glcnacase nagj (EC 3.2.1.169) | protein | 579 | 46% helix, 16% strand | Q0TR53 |
| T | TGF-beta-activated kinase 1 and MAP3K7-binding protein 1 | protein | 5 | 0% helix, 0% strand | Q15750 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains A, T
- CD · Cadmium ion · metal · 19 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 73 | 0.42 | 0.81 | 19 | CD |
| 2 | 125 | 0.41 | 0.75 | 15 | empty |
| 3 | 83 | 0.38 | 0.77 | 22 | empty |
| 4 | 79 | 0.36 | 0.76 | 16 | empty |
| 5 | 77 | 0.35 | 0.76 | 14 | CD |
Interfaces
1 interface between chains.
- A–T · 262 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 1 glycan (O-glycosylation).
Compared structures
- 2YDS · CpOGA D298N in complex with TAB1-derived O-GlcNAc peptide · the same entry in another collection · chain A against A, 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
- Q15750 · AlphaFold monomer V2.0 prediction for TGF-beta-activated kinase 1 and MAP3K7-binding… · a predicted model of the same protein · chain T against A, TM-score 0.56
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 Q15750
- Elsewhere: RCSB PDB 2YDS · PDBe 2YDS · UniProt Q0TR53 · UniProt Q15750
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.