Research workbench
Structure of human O-glcnac hydrolase with bound transition state analog thiametg
Analyse Structure of human O-glcnac hydrolase with bound transition state analog… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5M7S
- Type
- protein
- Length
- 887 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein O-glcnacase
- EC
- 3.2.1.169, 3.2.1.-
- UniProt
- O60502
- Ligands
- NHT
- Pockets
- 7 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 49% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein O-glcnacase (EC 3.2.1.169, 3.2.1.-) | protein | 443 | 50% helix, 9% strand | O60502 |
| B | Protein O-glcnacase (EC 3.2.1.169, 3.2.1.-) | protein | 444 | 49% helix, 9% strand | O60502 |
Ligands and binding sites
- NHT · (3ar,5r,6s,7r,7ar)-2-(ethylamino)-5-(hydroxymethyl)-5, 6,7,7A-tetrahydro-3AH-pyrano[3,2-d][1,3]thiazole-6,7-diol · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 831 | 0.82 | 0.85 | 74 | empty |
| 2 | 341 | 0.64 | 0.79 | 45 | NHT |
| 3 | 166 | 0.64 | 0.85 | 24 | empty |
| 4 | 331 | 0.63 | 0.79 | 41 | NHT |
| 5 | 180 | 0.54 | 0.79 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 4268 Ų buried · 36 hydrogen bonds · protein-protein
Compared structures
- 5M7S · Structure of human O-GlcNAc hydrolase with bound transition state analog ThiametG · the same entry in another collection · chain A against A, TM-score 1.00
- O60502 · AlphaFold monomer V2.0 prediction for protein O-glcnacase (O60502) · a predicted model of the same protein · chain B 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 5M7S · PDBe 5M7S · UniProt O60502
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