Research workbench
Udp-glcnac C4-epimerase mutant S121A/Y146F from pseudomonas protegens in complex with udp-glcnac
Analyse Udp-glcnac C4-epimerase mutant S121A/Y146F from pseudomonas protegens in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6WJ9
- Type
- protein
- Length
- 615 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NAD-dependent EPIMERASE/DEHYDRATASE family protein
- UniProt
- Q4KCF6
- Ligands
- NAD, UD1
- Pockets
- 3 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | NAD-dependent EPIMERASE/DEHYDRATASE family protein | protein | 307 | 41% helix, 20% strand | Q4KCF6 |
| B | NAD-dependent EPIMERASE/DEHYDRATASE family protein | protein | 308 | 41% helix, 19% strand | Q4KCF6 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 2 copies · chains A, B
- UD1 · Uridine-diphosphate-N-acetylglucosamine · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1120 | 0.82 | 0.83 | 84 | NAD, UD1 |
| 2 | 1109 | 0.81 | 0.82 | 84 | NAD, UD1 |
| 3 | 373 | 0.61 | 0.77 | 42 | empty |
Interfaces
1 interface between chains.
- A–B · 1038 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 6WJ9 · UDP-GlcNAc C4-epimerase mutant S121A/Y146F from Pseudomonas protegens in complex with… · the same entry in another collection · chain A 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 Q4KCF6
- Elsewhere: RCSB PDB 6WJ9 · PDBe 6WJ9 · UniProt Q4KCF6
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