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P. aeruginosa lpxa in complex with ligand H7

Analyse P. aeruginosa lpxa in complex with ligand H7 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7T5R
Type: protein
Length: 1,541 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Acyl-[acyl-carrier-protein]--udp-N-acetylglucosamine O- acyltransferase
EC: 2.3.1.129
UniProt: A6V1E4
Ligands: F30
Pockets: 20 · best druggability 0.74

Structure

x-ray diffraction · 2 distinct chains · 18% helix, 28% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, D, E, F	Acyl-[acyl-carrier-protein]--udp-N-acetylglucosamine O- acyltransferase (EC 2.3.1.129)	protein	257	18% helix, 28% strand	A6V1E4
C	Acyl-[acyl-carrier-protein]--udp-N-acetylglucosamine O- acyltransferase (EC 2.3.1.129)	protein	256	18% helix, 28% strand	A6V1E4

Ligands and binding sites

F30 · 3-bromo-N-[3-(1H-tetrazol-5-yl)phenyl]-1H-indole-5-carboxamide · ligand · 7 copies · chains A, B, C, D, F, E
GOL · Glycerol · additive · chains D

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

Pockets

20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	487	0.74	0.83	70	empty
2	104	0.72	0.93	21	empty
3	98	0.70	0.93	17	empty
4	152	0.69	0.89	25	F30
5	566	0.68	0.78	69	F30

Interfaces

8 interfaces between chains.

D–E · 1011 Å² buried · 10 hydrogen bonds · protein-protein
E–F · 1005 Å² buried · 12 hydrogen bonds · protein-protein
B–C · 1003 Å² buried · 13 hydrogen bonds · protein-protein
D–F · 997 Å² buried · 14 hydrogen bonds · protein-protein
A–C · 979 Å² buried · 12 hydrogen bonds · protein-protein

Compared structures

7T5R · P. aeruginosa LpxA in complex with ligand H7 · the same entry in another collection · chain F against F, TM-score 1.00
A6V1E4 · AlphaFold monomer V2.0 prediction for acyl-[acyl-carrier… · a predicted model of the same protein · chain C against A, TM-score 0.99

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 A6V1E4
Elsewhere: RCSB PDB 7T5R · PDBe 7T5R · UniProt A6V1E4

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