Research workbench
Cpoga D298N in complex with drosophila hcf -derived thr-O-glcnac peptide
Analyse Cpoga D298N in complex with drosophila hcf -derived thr-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
- 4ZXL
- Type
- protein
- Length
- 583 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nag-pro-ser-thr-ala-thr-O-glcnac containing peptide from drosophila hcf; O-glcnacase nagj
- EC
- 3.2.1.169, 3.2.1.52
- UniProt
- Q0TR53
- Ligands
- NAG, CD
- Pockets
- 7 · best druggability 0.45
Structure
x-ray diffraction · 2 distinct chains · 46% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | Nag-pro-ser-thr-ala-thr-O-glcnac containing peptide from drosophila hcf | protein | 4 | 0% helix, 0% strand | — |
| A | O-glcnacase nagj (EC 3.2.1.169, 3.2.1.52) | protein | 579 | 46% helix, 15% strand | Q0TR53 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains H, A
- CD · Cadmium ion · metal · 15 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 | 80 | 0.45 | 0.81 | 19 | empty |
| 2 | 137 | 0.41 | 0.74 | 16 | empty |
| 3 | 102 | 0.37 | 0.75 | 18 | empty |
| 4 | 58 | 0.36 | 0.79 | 16 | empty |
| 5 | 51 | 0.35 | 0.79 | 14 | empty |
Interfaces
1 interface between chains.
- H–A · 245 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 glycan (O-glycosylation).
Compared structures
- 4ZXL · CpOGA D298N in complex with Drosophila HCF -derived Thr-O-GlcNAc peptide · the same entry in another collection · chain H against H, 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
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
- Elsewhere: RCSB PDB 4ZXL · PDBe 4ZXL · UniProt Q0TR53
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