MolNFT v1 · #163621 · protein

Cryo-EM structure of LPTB2FG in complex with lps

6S8H · Lipopolysaccharide ABC transporter, ATP-binding protein lptb: “Cryo-EM structure of LPTB2FG in complex with lps”. Electron microscopy, 3 ligands (LMN, DCQ, JSG), 7 pockets (best druggability 0.74). MolNFT v1 #163621 on GenesisL1: 3D…

PDB: 6S8H
Type: protein
Length: 959 residues
Chains: 4
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Lipopolysaccharide ABC transporter, ATP-binding protein lptb; Lipopolysaccharide export…
UniProt: E7T9E6, P0AFA1, A0A2S4N3I3
Ligands: LMN, DCQ, JSG
Pockets: 7 · best druggability 0.74

Structure

electron microscopy · 4 distinct chains · 40% helix, 10% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Lipopolysaccharide ABC transporter, ATP-binding protein lptb	protein	239	21% helix, 19% strand	E7T9E6
B	Lipopolysaccharide ABC transporter, ATP-binding protein lptb	protein	238	27% helix, 22% strand	E7T9E6
F	Lipopolysaccharide export system permease protein lptf	protein	239	51% helix, 0% strand	P0AFA1
G	Inner membrane protein yjgq	protein	243	59% helix, 0% strand	A0A2S4N3I3

Ligands and binding sites

LMN · Lauryl Maltose Neopentyl Glycol · ligand · 2 copies · chains F, G
DCQ · 2-decyl-5,6-dimethoxy-3-methylcyclohexa-2,5-diene-1,4-dione · ligand · 2 copies · chains F, G
JSG · (2~{R},4~{R},5~{R},6~{R})-6-[(1~{R})-1,2-bis(oxidanyl) ethyl]-2-[(2~{R},4~{R},5~{R},6~{R})-6-[(1~{R})-1,2-bis(oxidanyl)ethyl]-5-[(2~{S},3~{S},4~{R},5~{R}, 6~{R})-6-[(1~{S})-1,2-bis(oxidanyl)ethyl]-4-[(2~{R}, 3~{S},4~{R},5~{S},6~{R})-6-[(1~{S})-2-[(2~{S},3~{S}, 4~{S},5~{S},6~{R})-6-[(1~{S})-1,2-bis(oxidanyl)ethyl]-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-1-oxidanyl-ethyl]-3, 4-bis(oxidanyl)-5-phosphonooxy-oxan-2-yl]oxy-3-oxidanyl-5-phosphonooxy-oxan-2-yl]oxy-2-carboxy-2-[[(2~{R},3~{S},4~{R},5~{R},6~{R}) · ligand · chains F, G
LMT · Dodecyl-beta-D-maltoside · additive · 2 copies · chains F, G

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	599	0.74	0.80	78	LMN
2	474	0.69	0.80	54	empty
3	481	0.65	0.77	41	empty
4	379	0.57	0.75	46	empty
5	139	0.57	0.83	22	empty

Interfaces

4 interfaces between chains.

B–F · 994 Å² buried · 4 hydrogen bonds · protein-protein
A–G · 947 Å² buried · 6 hydrogen bonds · protein-protein
F–G · 744 Å² buried · 3 hydrogen bonds · protein-protein
A–B · 631 Å² buried · 6 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 3 covalent (covalent ligand, additive adduct).

Compared structures

6S8H · Cryo-EM structure of LptB2FG in complex with LPS · the same entry in another collection · chain A against A, TM-score 1.00
P0AFA1 · AlphaFold monomer V2.0 prediction for lipopolysaccharide export system permease protein… · a predicted model of the same protein · chain F against A, TM-score 0.96

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 E7T9E6
Every structure of UniProt P0AFA1
Every structure of UniProt A0A2S4N3I3
Elsewhere: RCSB PDB 6S8H · PDBe 6S8H · UniProt E7T9E6 · UniProt P0AFA1 · UniProt A0A2S4N3I3

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