Research workbench

Lptbfgc from enterobacter cloacae

Analyse Lptbfgc from enterobacter cloacae in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6MIT
Type: protein
Length: 2,657 residues
Chains: 10
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Lipopolysaccharide export system ATP-binding protein; Lipopolysaccharide export system…
UniProt: A0A0H3CR83, A0A0H3CU18, A0A232G4N0, A0A0H3CQA2
Ligands: NOV, SO4, CL
Pockets: 20 · best druggability 0.74

Structure

x-ray diffraction · 7 distinct chains · 52% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, D	Lipopolysaccharide export system ATP-binding protein	protein	240	37% helix, 22% strand	A0A0H3CR83
C, H	Lipopolysaccharide export system protein lptc	protein	175	12% helix, 54% strand	A0A0H3CU18
F	Lps export ABC transporter permease lptf	protein	350	59% helix, 15% strand	A0A232G4N0
G	Lipopolysaccharide export system permease protein lptg	protein	355	63% helix, 15% strand	A0A0H3CQA2
E	Lipopolysaccharide export system ATP-binding protein	protein	238	40% helix, 26% strand	A0A0H3CR83
I	Lps export ABC transporter permease lptf	protein	335	60% helix, 13% strand	A0A232G4N0
J	Lipopolysaccharide export system permease protein lptg	protein	309	70% helix, 7% strand	A0A0H3CQA2

Ligands and binding sites

NOV · Novobiocin · ligand · chains B, E
SO4 · Sulfate ion · ion · 11 copies · chains A, B, F, G, D, E, I, J
CL · Chloride ion · ion · chains A

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

Pockets

20 pockets found on a 1 Å grid, 19 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	517	0.74	0.82	55	empty
2	438	0.74	0.83	47	empty
3	830	0.73	0.78	83	empty
4	1120	0.73	0.76	106	SO4
5	679	0.73	0.79	79	empty

Interfaces

15 interfaces between chains.

C–F · 1298 Å² buried · 15 hydrogen bonds · protein-protein
F–G · 1281 Å² buried · 5 hydrogen bonds · protein-protein
H–I · 1227 Å² buried · 14 hydrogen bonds · protein-protein
B–F · 1065 Å² buried · 10 hydrogen bonds · protein-protein
E–I · 1049 Å² buried · 8 hydrogen bonds · protein-protein

Compared structures

6MIT · LptBFGC from Enterobacter cloacae · the same entry in another collection · chain I against I, 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 A0A0H3CR83
Every structure of UniProt A0A0H3CU18
Every structure of UniProt A0A232G4N0
Every structure of UniProt A0A0H3CQA2
Elsewhere: RCSB PDB 6MIT · PDBe 6MIT · UniProt A0A0H3CR83 · UniProt A0A0H3CU18 · UniProt A0A232G4N0 · UniProt A0A0H3CQA2

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.