Research workbench
Crystal structure of a selenomethionine derivative of E. COLI lptb in complex with ADP-magensium
Analyse Crystal structure of a selenomethionine derivative of E. COLI lptb in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4P31
- 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 0.85
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 | 38% helix, 28% strand | P0A9V1 |
| B | Lipopolysaccharide export system ATP-binding protein lptb (EC 3.6.3.-) | protein | 230 | 36% helix, 29% 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 | 1134 | 0.85 | 0.86 | 75 | empty |
| 2 | 114 | 0.39 | 0.75 | 20 | empty |
| 3 | 112 | 0.39 | 0.76 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 924 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 modified (engineered).
Compared structures
- 4P31 · Crystal structure of a selenomethionine derivative of E. coli LptB in complex with… · 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 4P31 · PDBe 4P31 · UniProt P0A9V1
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