Research workbench
Specific recognition of N-acetylated substrates and domain flexibility in wbgu: a udp-galnac 4-epimerase
Analyse Specific recognition of N-acetylated substrates and domain flexibility in wbgu… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3RU9
- 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, GLY, SO4
- Pockets
- 11 · best druggability 0.86
Structure
x-ray diffraction · 1 distinct chain · 48% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Wbgu | protein | 336 | 48% helix, 15% 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
- GLY · Glycine · ligand · 2 copies · chains C, D
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1109 | 0.86 | 0.87 | 105 | NAD, UNL |
| 2 | 1091 | 0.85 | 0.86 | 93 | NAD, UNL |
| 3 | 987 | 0.85 | 0.86 | 83 | NAD, UNL |
| 4 | 1012 | 0.83 | 0.84 | 80 | NAD, UNL |
| 5 | 743 | 0.70 | 0.77 | 80 | empty |
Interfaces
5 interfaces between chains.
- A–C · 1207 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 798 Ų buried · 18 hydrogen bonds · protein-protein
- C–D · 548 Ų buried · 5 hydrogen bonds · protein-protein
- A–D · 114 Ų buried · 2 hydrogen bonds · protein-protein
- B–D · 51 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3RU9 · Specific recognition of N-acetylated substrates and domain flexibility in WbgU: a… · the same entry in another collection · chain D against D, 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 B 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 3RU9 · PDBe 3RU9 · UniProt Q7BJX9
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