Research workbench
E. coli heptosyltransferase WaaC with ADP-2-deoxy-2-fluoro heptose
Analyse E. coli heptosyltransferase WaaC with ADP-2-deoxy-2-fluoro heptose in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2H1H
- Type
- protein
- Length
- 637 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.4
- Source
- Escherichia coli
- Molecule
- Lipopolysaccharide heptosyltransferase 1
- EC
- 2.-.-.-
- UniProt
- P24173
- Ligands
- AFH
- Pockets
- 6 · best druggability 0.72
Structure
x-ray diffraction · resolution 2.4 · 2 distinct chains · 42% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lipopolysaccharide heptosyltransferase 1 (EC 2.-.-.-) | protein | 322 | 44% helix, 18% strand | P24173 |
| B | Lipopolysaccharide heptosyltransferase 1 (EC 2.-.-.-) | protein | 315 | 41% helix, 18% strand | P24173 |
Ligands and binding sites
- AFH · Adenosine-5'-diphosphate-2-deoxy-2-fluoro heptose · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 899 | 0.72 | 0.77 | 101 | AFH |
| 2 | 165 | 0.48 | 0.76 | 26 | AFH |
| 3 | 200 | 0.45 | 0.74 | 36 | empty |
| 4 | 101 | 0.45 | 0.79 | 23 | empty |
| 5 | 103 | 0.40 | 0.77 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 563 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 2H1H · E. COLI heptosyltransferase waac with ADP-2-deoxy-2-fluoro heptose · the same entry in another collection · chain A against A, TM-score 1.00
- P24173 · AlphaFold monomer V2.0 prediction for lipopolysaccharide heptosyltransferase 1 (P24173) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 P24173
- Elsewhere: RCSB PDB 2H1H · PDBe 2H1H · UniProt P24173
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