Research workbench
Alternative analogs as viable substrates of udp-hexose 4-epimerases
Analyse Alternative analogs as viable substrates of udp-hexose 4-epimerases in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3RUD
- Type
- protein
- Length
- 1,344 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Wbgu
- UniProt
- Q7BJX9
- Ligands
- NAD, UNL
- Pockets
- 10 · best druggability 0.86
Structure
x-ray diffraction · 1 distinct chain · 47% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Wbgu | protein | 336 | 47% helix, 16% strand | Q7BJX9 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 4 copies · chains A, B, C, D
- UNL · Unknown ligand · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1130 | 0.86 | 0.87 | 100 | NAD, UNL |
| 2 | 992 | 0.85 | 0.86 | 90 | NAD, UNL |
| 3 | 788 | 0.85 | 0.88 | 73 | NAD, UNL |
| 4 | 1010 | 0.83 | 0.84 | 88 | NAD, UNL |
| 5 | 1026 | 0.70 | 0.74 | 85 | empty |
Interfaces
4 interfaces between chains.
- B–C · 1194 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 786 Ų buried · 16 hydrogen bonds · protein-protein
- C–D · 488 Ų buried · 3 hydrogen bonds · protein-protein
- B–D · 112 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 3RUD · Alternative analogs as viable substrates of UDP-hexose 4-epimerases · the same entry in another collection · chain A against A, TM-score 1.00
- Q7BJX9 · AlphaFold monomer V2.0 prediction for udp-N-acetylglucosamine 4-epimerase (Q7BJX9) · a predicted model of the same protein · chain A 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 Q7BJX9
- Elsewhere: RCSB PDB 3RUD · PDBe 3RUD · UniProt Q7BJX9
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