Research workbench

E. COLI msba in complex with lps and inhibitor G092

Analyse E. COLI msba in complex with lps and inhibitor G092 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6BPP
Type: protein
Length: 1,137 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Lipid a export ATP-BINDING/PERMEASE protein msba
EC: 3.6.3.-
UniProt: Q8FJB1
Ligands: 3PE, FTT, E1M, PA1, DAO, MYR, GMH, GLC, KDO, GCS, PO4
Pockets: 13 · best druggability 0.83

Structure

x-ray diffraction · 2 distinct chains · 66% helix, 10% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Lipid a export ATP-BINDING/PERMEASE protein msba (EC 3.6.3.-)	protein	576	66% helix, 10% strand	Q8FJB1
B	Lipid a export ATP-BINDING/PERMEASE protein msba (EC 3.6.3.-)	protein	561	65% helix, 10% strand	Q8FJB1

Ligands and binding sites

3PE · 1,2-diacyl-sn-glycero-3-phosphoethanolamine · ligand · 7 copies · chains A, B
FTT · 3-hydroxy-tetradecanoic acid · ligand · 4 copies · chains A, B
E1M · (2E)-3-{6-[(1S)-1-(3-amino-2,6-dichlorophenyl)ethoxy]-4-cyclopropylquinolin-3-yl}prop-2-enoic acid · ligand · 2 copies · chains A, B
PA1 · 2-amino-2-deoxy-alpha-D-glucopyranose · ligand · chains B
DAO · Lauric acid · ligand · chains A, B
MYR · Myristic acid · ligand · chains A, B
GMH · L-glycero-alpha-D-manno-heptopyranose · sugar · 3 copies · chains B
GLC · alpha-D-glucopyranose · sugar · 3 copies · chains A
KDO · 3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid · sugar · 2 copies · chains B
GCS · 2-amino-2-deoxy-beta-D-glucopyranose · sugar · chains A, B
PO4 · Phosphate ion · ion · 2 copies · chains B, A

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

13 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	829	0.83	0.85	58	FTT, DAO, MYR
2	1020	0.80	0.82	120	empty
3	185	0.68	0.86	23	E1M
4	225	0.63	0.82	25	E1M
5	115	0.61	0.86	25	empty

Interfaces

1 interface between chains.

A–B · 5699 Å² buried · 30 hydrogen bonds · protein-protein

Compared structures

6BPP · E. coli MsbA in complex with LPS and inhibitor G092 · the same entry in another collection · chain A against A, TM-score 1.00
Q8FJB1 · AlphaFold monomer V2.0 prediction for ATP-dependent lipid a-core flippase (Q8FJB1) · a predicted model of the same protein · chain B against A, TM-score 0.94

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 Q8FJB1
Elsewhere: RCSB PDB 6BPP · PDBe 6BPP · UniProt Q8FJB1

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