Research workbench
Crystal structure of human O-glcnacase in complex with glycopeptide P53
Analyse Crystal structure of human O-glcnacase in complex with glycopeptide P53 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5UN8
- Type
- protein
- Length
- 1,740 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein O-glcnacase; P53 peptide
- EC
- 3.2.1.169, 3.2.1.-
- UniProt
- O60502
- Ligands
- NAG
- Pockets
- 16 · best druggability 0.82
Structure
x-ray diffraction · 6 distinct chains · 50% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein O-glcnacase (EC 3.2.1.169, 3.2.1.-) | protein | 424 | 50% helix, 9% strand | O60502 |
| B | Protein O-glcnacase (EC 3.2.1.169, 3.2.1.-) | protein | 426 | 51% helix, 9% strand | O60502 |
| C, D | Protein O-glcnacase (EC 3.2.1.169, 3.2.1.-) | protein | 429 | 51% helix, 9% strand | O60502 |
| E | P53 peptide | protein | 7 | 0% helix, 0% strand | — |
| F, H | P53 peptide | protein | 8 | 0% helix, 0% strand | — |
| G | P53 peptide | protein | 9 | 0% helix, 22% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, C, E, B, D, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 992 | 0.82 | 0.83 | 74 | empty |
| 2 | 1020 | 0.82 | 0.83 | 82 | empty |
| 3 | 451 | 0.73 | 0.83 | 59 | NAG |
| 4 | 404 | 0.72 | 0.83 | 53 | NAG |
| 5 | 57 | 0.72 | 0.98 | 23 | NAG |
Interfaces
10 interfaces between chains.
- A–C · 3592 Ų buried · 36 hydrogen bonds · protein-protein
- B–D · 3591 Ų buried · 33 hydrogen bonds · protein-protein
- D–H · 329 Ų buried · 1 hydrogen bond · protein-protein
- C–G · 322 Ų buried · 2 hydrogen bonds · protein-protein
- A–E · 269 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 glycan (O-glycosylation).
Compared structures
- 5UN8 · Crystal Structure of human O-GlcNAcase in complex with glycopeptide p53 · the same entry in another collection · chain H against H, TM-score 1.00
- O60502 · AlphaFold monomer V2.0 prediction for protein O-glcnacase (O60502) · a predicted model of the same protein · chain C against A, TM-score 0.95
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 O60502
- Elsewhere: RCSB PDB 5UN8 · PDBe 5UN8 · UniProt O60502
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