MolNFT v1 · #136067 · protein
Crystal structure of the core catalytic domain of human O-glcnacase
5UHP · O-glcnacase tim-barrel domain: “Crystal structure of the core catalytic domain of human O-glcnacase”. X-ray diffraction, 20 pockets (best druggability 0.79). MolNFT v1 #136067 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 5UHP
- Type
- protein
- Length
- 1,681 residues
- Chains
- 8
- 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
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · 7 distinct chains · 50% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | O-glcnacase tim-barrel domain (EC 3.2.1.169, 3.2.1.-) | protein | 307 | 40% helix, 12% strand | O60502 |
| C | O-glcnacase tim-barrel domain (EC 3.2.1.169, 3.2.1.-) | protein | 310 | 39% helix, 12% strand | O60502 |
| D | O-glcnacase tim-barrel domain (EC 3.2.1.169, 3.2.1.-) | protein | 310 | 40% helix, 12% strand | O60502 |
| E | O-glcnacase stalk domain (EC 3.2.1.169, 3.2.1.-) | protein | 112 | 70% helix, 0% strand | O60502 |
| F | O-glcnacase stalk domain (EC 3.2.1.169, 3.2.1.-) | protein | 109 | 75% helix, 3% strand | O60502 |
| G | O-glcnacase stalk domain (EC 3.2.1.169, 3.2.1.-) | protein | 114 | 70% helix, 3% strand | O60502 |
| H | O-glcnacase stalk domain (EC 3.2.1.169, 3.2.1.-) | protein | 112 | 74% helix, 0% strand | O60502 |
Ligands and binding sites
- GOL · Glycerol · additive · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 145 | 0.79 | 0.95 | 25 | empty |
| 2 | 874 | 0.78 | 0.81 | 65 | empty |
| 3 | 250 | 0.74 | 0.88 | 33 | empty |
| 4 | 830 | 0.71 | 0.77 | 58 | empty |
| 5 | 482 | 0.68 | 0.79 | 41 | empty |
Interfaces
19 interfaces between chains.
- B–G · 1485 Ų buried · 18 hydrogen bonds · protein-protein
- A–F · 1480 Ų buried · 23 hydrogen bonds · protein-protein
- C–H · 1311 Ų buried · 12 hydrogen bonds · protein-protein
- D–E · 1305 Ų buried · 10 hydrogen bonds · protein-protein
- E–H · 1269 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
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 5UHP · PDBe 5UHP · UniProt O60502
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