MolNFT v1 · #136066 · protein
Crystal structure of the core catalytic domain of human O-glcnacase complexed with pugnac
5UHO · O-glcnacase tim-barrel domain: “Crystal structure of the core catalytic domain of human O-glcnacase complexed with pugnac”. X-ray diffraction, 1 ligand (OAN), 5 pockets (best druggability 0.81). MolNFT v1 #136066 on GenesisL1: 3D…
- PDB
- 5UHO
- 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
- OAN
- Pockets
- 5 · best druggability 0.81
Structure
x-ray diffraction · 4 distinct chains · 49% 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 | 41% helix, 13% strand | O60502 |
| B | O-glcnacase stalk domain (EC 3.2.1.169, 3.2.1.-) | protein | 120 | 70% helix, 2% 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 | 66% helix, 0% strand | O60502 |
Ligands and binding sites
- OAN · O-(2-acetamido-2-deoxy D-glucopyranosylidene) amino-N-phenylcarbamate · ligand · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 843 | 0.81 | 0.83 | 99 | empty |
| 2 | 285 | 0.61 | 0.79 | 37 | OAN |
| 3 | 234 | 0.59 | 0.79 | 33 | OAN |
| 4 | 118 | 0.49 | 0.80 | 19 | empty |
| 5 | 194 | 0.47 | 0.75 | 20 | empty |
Interfaces
6 interfaces between chains.
- C–D · 1318 Ų buried · 14 hydrogen bonds · protein-protein
- B–D · 1315 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 1310 Ų buried · 14 hydrogen bonds · protein-protein
- A–D · 1109 Ų buried · 16 hydrogen bonds · protein-protein
- B–C · 1076 Ų buried · 20 hydrogen bonds · protein-protein
Compared structures
- 5UHO · Crystal structure of the core catalytic domain of human O-GlcNAcase complexed with PUGNAc · the same entry in another collection · chain C against C, 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 5UHO · PDBe 5UHO · UniProt O60502
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