MolNFT v1 · #40523 · protein
Crystal structure of waag, a glycosyltransferase involved in lipopolysaccharide biosynthesis
2IV7 · Lipopolysaccharide core biosynthesis protein rfag: “Crystal structure of waag, a glycosyltransferase involved in lipopolysaccharide biosynthesis”. X-ray diffraction, 1 ligand (UDP), 3 pockets (best druggability 0.75). MolNFT v1…
- PDB
- 2IV7
- Type
- protein
- Length
- 370 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lipopolysaccharide core biosynthesis protein rfag
- UniProt
- P25740
- Ligands
- UDP
- Pockets
- 3 · best druggability 0.75
Structure
x-ray diffraction · 1 distinct chain · 48% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lipopolysaccharide core biosynthesis protein rfag | protein | 370 | 48% helix, 16% strand | P25740 |
Ligands and binding sites
- UDP · Uridine-5'-diphosphate · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 691 | 0.75 | 0.81 | 61 | UDP |
| 2 | 104 | 0.49 | 0.81 | 19 | empty |
| 3 | 123 | 0.42 | 0.76 | 19 | empty |
Modifications
Observed in the structure: 6 modified (engineered).
Compared structures
- 2IV7 · Crystal Structure of WaaG, a glycosyltransferase involved in lipopolysaccharide… · the same entry in another collection · chain A against A, TM-score 1.00
- P25740 · AlphaFold monomer V2.0 prediction for lipopolysaccharide core biosynthesis protein rfag… · a predicted model of the same protein · 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 P25740
- Elsewhere: RCSB PDB 2IV7 · PDBe 2IV7 · UniProt P25740
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