Research workbench
Crystal structure analysis of wbgu: a udp-galnac 4-epimerase
Analyse Crystal structure analysis of wbgu: a udp-galnac 4-epimerase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3LU1
- Type
- protein
- Length
- 1,340 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Wbgu
- EC
- 5.1.3.7
- UniProt
- Q7BJX9
- Ligands
- NAD, UD2, GLY, NA, SO4
- Pockets
- 11 · best druggability 0.87
Structure
x-ray diffraction · 2 distinct chains · 47% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Wbgu (EC 5.1.3.7) | protein | 336 | 47% helix, 16% strand | Q7BJX9 |
| B, C | Wbgu (EC 5.1.3.7) | protein | 334 | 46% helix, 16% strand | Q7BJX9 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 4 copies · chains A, B, C, D
- UD2 · Uridine-diphosphate-N-acetylgalactosamine · ligand · 4 copies · chains A, B, C, D
- GLY · Glycine · ligand · 4 copies · chains A, B, C, D
- NA · Sodium ion · metal · chains D
- SO4 · Sulfate ion · ion · 3 copies · chains C, D, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 734 | 0.87 | 0.90 | 81 | NAD, UD2 |
| 2 | 1114 | 0.86 | 0.87 | 102 | NAD, UD2 |
| 3 | 718 | 0.85 | 0.88 | 73 | NAD, UD2 |
| 4 | 777 | 0.84 | 0.87 | 70 | NAD, UD2 |
| 5 | 782 | 0.70 | 0.76 | 67 | empty |
Interfaces
4 interfaces between chains.
- B–D · 1222 Ų buried · 6 hydrogen bonds · protein-protein
- A–D · 804 Ų buried · 13 hydrogen bonds · protein-protein
- B–C · 561 Ų buried · 2 hydrogen bonds · protein-protein
- C–D · 103 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 3LU1 · Crystal Structure Analysis of WbgU: a UDP-GalNAc 4-epimerase · 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 1.00
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 3LU1 · PDBe 3LU1 · UniProt Q7BJX9
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.