MolNFT v1 · #77955 · protein
Specific recognition of N-acetylated substrates and domain flexibility in wbgu: a udp-galnac 4-epimerase
3RUA: “Specific recognition of N-acetylated substrates and domain flexibility in wbgu: a udp-galnac 4-epimerase”. X-ray diffraction, 3 ligands (NAD, UNL, SO4), 7 pockets (best druggability 0.86). MolNFT v1 #77955 on GenesisL1: 3D…
- PDB
- 3RUA
- 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, SO4
- Pockets
- 7 · 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
- 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
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 | 1131 | 0.86 | 0.87 | 107 | NAD, UNL |
| 2 | 809 | 0.85 | 0.88 | 75 | NAD, UNL |
| 3 | 1056 | 0.85 | 0.86 | 91 | NAD, UNL |
| 4 | 948 | 0.84 | 0.85 | 77 | NAD, UNL |
| 5 | 1124 | 0.70 | 0.75 | 102 | empty |
Interfaces
4 interfaces between chains.
- B–C · 1186 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 799 Ų buried · 18 hydrogen bonds · protein-protein
- C–D · 540 Ų buried · 3 hydrogen bonds · protein-protein
- B–D · 117 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 3RUA · Specific recognition of N-acetylated substrates and domain flexibility in WbgU: a… · 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 3RUA · PDBe 3RUA · UniProt Q7BJX9
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