Research workbench
Crystal structure of E. COLI lptb-E163Q in complex with ATP-sodium
Analyse Crystal structure of E. COLI lptb-E163Q in complex with ATP-sodium in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4P33
- Type
- protein
- Length
- 470 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lipopolysaccharide export system ATP-binding protein lptb
- EC
- 3.6.3.-
- UniProt
- P0A9V1
- Ligands
- ATP, NA
- Pockets
- 4 · best druggability 0.85
Structure
x-ray diffraction · 1 distinct chain · 40% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Lipopolysaccharide export system ATP-binding protein lptb (EC 3.6.3.-) | protein | 235 | 40% helix, 28% strand | P0A9V1 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 2 copies · chains A, B
- NA · Sodium ion · metal · 2 copies · chains A, B
- GOL · Glycerol · additive · 5 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1087 | 0.85 | 0.85 | 79 | GOL |
| 2 | 133 | 0.45 | 0.77 | 20 | GOL |
| 3 | 124 | 0.41 | 0.75 | 23 | GOL |
| 4 | 67 | 0.29 | 0.74 | 18 | GOL, NA, ATP |
Interfaces
1 interface between chains.
- A–B · 943 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 4P33 · Crystal structure of E. coli LptB-E163Q in complex with ATP-sodium · the same entry in another collection · chain A against A, TM-score 1.00
- P0A9V1 · AlphaFold monomer V2.0 prediction for lipopolysaccharide export system ATP-binding… · a predicted model of the same protein · chain A against A, TM-score 0.95
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 P0A9V1
- Elsewhere: RCSB PDB 4P33 · PDBe 4P33 · UniProt P0A9V1
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