MolNFT v1 · #177346 · protein

LPTB2FG-lps from klebsiella pneumoniae in nanodiscs

7EFO · Lipopolysaccharide export system ATP-binding protein lptb: “LPTB2FG-lps from klebsiella pneumoniae in nanodiscs”. Electron microscopy, 1 ligand (JSG), 7 pockets (best druggability 0.76). MolNFT v1 #177346 on GenesisL1: 3D structure…

PDB: 7EFO
Type: protein
Length: 916 residues
Chains: 4
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Lipopolysaccharide export system ATP-binding protein lptb; Lipopolysaccharide export…
UniProt: A0A2X3II39, A0A1Y0Q3P9, A0A1Y0Q3C0
Ligands: JSG
Pockets: 7 · best druggability 0.76

Structure

electron microscopy · 4 distinct chains · 55% helix, 11% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Lipopolysaccharide export system ATP-binding protein lptb	protein	235	37% helix, 20% strand	A0A2X3II39
B	Lipopolysaccharide export system ATP-binding protein lptb	protein	237	35% helix, 24% strand	A0A2X3II39
F	Lipopolysaccharide export system permease protein lptf	protein	219	74% helix, 0% strand	A0A1Y0Q3P9
G	Lps export ABC transporter permease lptg	protein	225	76% helix, 0% strand	A0A1Y0Q3C0

Ligands and binding sites

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

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	1136	0.76	0.78	73	JSG
2	854	0.76	0.80	106	empty
3	452	0.64	0.77	46	empty
4	335	0.60	0.77	41	empty
5	73	0.50	0.84	14	empty

Interfaces

4 interfaces between chains.

B–F · 1029 Å² buried · 12 hydrogen bonds · protein-protein
A–G · 1022 Å² buried · 3 hydrogen bonds · protein-protein
F–G · 760 Å² buried · 4 hydrogen bonds · protein-protein
A–B · 581 Å² buried · 3 hydrogen bonds · protein-protein

Compared structures

7EFO · LptB2FG-LPS from Klebsiella pneumoniae in nanodiscs · the same entry in another collection · chain A against A, TM-score 1.00

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 A0A2X3II39
Every structure of UniProt A0A1Y0Q3P9
Every structure of UniProt A0A1Y0Q3C0
Elsewhere: RCSB PDB 7EFO · PDBe 7EFO · UniProt A0A2X3II39 · UniProt A0A1Y0Q3P9 · UniProt A0A1Y0Q3C0

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