Research workbench

E. COLI lptb in complex with ADP and novobiocin

Analyse E. COLI lptb in complex with ADP and novobiocin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6B89
Type: protein
Length: 460 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, NOV, MG
Pockets: 5 · 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	37% helix, 28% strand	P0A9V1
B	Lipopolysaccharide export system ATP-binding protein lptb (EC 3.6.3.-)	protein	226	38% helix, 29% strand	P0A9V1

Ligands and binding sites

ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains A, B
NOV · Novobiocin · 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

5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1097	0.85	0.86	94	ADP, MG, NOV
2	55	0.39	0.81	15	empty
3	96	0.39	0.77	17	empty
4	109	0.38	0.75	17	empty
5	69	0.37	0.78	13	empty

Interfaces

1 interface between chains.

A–B · 1080 Å² buried · 6 hydrogen bonds · protein-protein

Compared structures

6B89 · E. coli LptB in complex with ADP and novobiocin · 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 0.97

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 6B89 · PDBe 6B89 · UniProt P0A9V1

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