MolNFT v1 · #102998 · protein
Crystal structure of E. COLI lptb in complex with ADP-magnesium
4P32 · Lipopolysaccharide export system ATP-binding protein lptb: “Crystal structure of E. COLI lptb in complex with ADP-magnesium”. X-ray diffraction, 2 ligands (ADP, MG), 3 pockets (best druggability 0.84). MolNFT v1 #102998 on…
- PDB
- 4P32
- Type
- protein
- Length
- 464 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
- ADP, MG
- Pockets
- 3 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lipopolysaccharide export system ATP-binding protein lptb (EC 3.6.3.-) | protein | 234 | 37% helix, 28% strand | P0A9V1 |
| B | Lipopolysaccharide export system ATP-binding protein lptb (EC 3.6.3.-) | protein | 230 | 36% helix, 28% strand | P0A9V1 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1121 | 0.84 | 0.85 | 74 | empty |
| 2 | 112 | 0.41 | 0.77 | 21 | empty |
| 3 | 126 | 0.39 | 0.74 | 24 | empty |
Interfaces
1 interface between chains.
- A–B · 882 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 4P32 · Crystal structure of E. coli LptB in complex with ADP-magnesium · 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 B 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 P0A9V1
- Elsewhere: RCSB PDB 4P32 · PDBe 4P32 · UniProt P0A9V1
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