Research workbench
Crystal structure of the core catalytic domain of human O-glcnacase complexed with thiamet G
Analyse Crystal structure of the core catalytic domain of human O-glcnacase complexed… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5UHL
- Type
- protein
- Length
- 846 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- O-glcnacase tim-barrel domain; O-glcnacase stalk domain
- EC
- 3.2.1.169, 3.2.1.-
- UniProt
- O60502
- Ligands
- 8BJ
- Pockets
- 8 · best druggability 0.79
Structure
x-ray diffraction · 4 distinct chains · 50% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | O-glcnacase tim-barrel domain (EC 3.2.1.169, 3.2.1.-) | protein | 304 | 42% helix, 12% strand | O60502 |
| B | O-glcnacase stalk domain (EC 3.2.1.169, 3.2.1.-) | protein | 120 | 69% helix, 0% strand | O60502 |
| C | O-glcnacase tim-barrel domain (EC 3.2.1.169, 3.2.1.-) | protein | 302 | 42% helix, 13% strand | O60502 |
| D | O-glcnacase stalk domain (EC 3.2.1.169, 3.2.1.-) | protein | 120 | 68% helix, 0% strand | O60502 |
Ligands and binding sites
- 8BJ · (2z,3ar,5r,6s,7r,7ar)-2-(ethylimino)-5-(hydroxymethyl) hexahydro-3AH-pyrano[3,2-d][1,3]thiazole-6,7-diol · ligand · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 529 | 0.79 | 0.86 | 61 | empty |
| 2 | 265 | 0.60 | 0.79 | 36 | 8BJ |
| 3 | 264 | 0.59 | 0.78 | 37 | 8BJ |
| 4 | 139 | 0.55 | 0.82 | 21 | empty |
| 5 | 50 | 0.53 | 0.89 | 22 | empty |
Interfaces
6 interfaces between chains.
- C–D · 1327 Ų buried · 14 hydrogen bonds · protein-protein
- B–D · 1317 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 1316 Ų buried · 16 hydrogen bonds · protein-protein
- B–C · 1121 Ų buried · 18 hydrogen bonds · protein-protein
- A–D · 1057 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 5UHL · Crystal structure of the core catalytic domain of human O-GlcNAcase complexed with… · the same entry in another collection · chain D against D, 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 0.99
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 O60502
- Elsewhere: RCSB PDB 5UHL · PDBe 5UHL · UniProt O60502
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