Research workbench
X-ray structure of H243I mutant of udp-galactose 4-epimerase from E.COLI:EVIDENCE for existence of open and closed active site during catalysis.
Analyse X-ray structure of H243I mutant of udp-galactose 4-epimerase from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5GY7
- Type
- protein
- Length
- 676 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Udp-glucose 4-epimerase
- EC
- 5.1.3.2
- UniProt
- P09147
- Ligands
- UDP, NAD, NO3
- Pockets
- 4 · best druggability 0.85
Structure
x-ray diffraction · 1 distinct chain · 42% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Udp-glucose 4-epimerase (EC 5.1.3.2) | protein | 338 | 42% helix, 18% strand | P09147 |
Ligands and binding sites
- UDP · Uridine-5'-diphosphate · ligand · 2 copies · chains A, B
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 2 copies · chains A, B
- NO3 · Nitrate ion · ion · chains B
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 561 | 0.85 | 0.91 | 78 | UDP, NAD |
| 2 | 570 | 0.85 | 0.90 | 81 | UDP, NAD |
| 3 | 180 | 0.50 | 0.77 | 27 | empty |
| 4 | 51 | 0.25 | 0.73 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 911 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 5GY7 · X-Ray structure of H243I mutant of UDP-Galactose 4-epimerase from E.coli:evidence for… · the same entry in another collection · chain A against A, TM-score 1.00
- P09147 · AlphaFold monomer V2.0 prediction for udp-glucose 4-epimerase (P09147) · 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 P09147
- Elsewhere: RCSB PDB 5GY7 · PDBe 5GY7 · UniProt P09147
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