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P. aeruginosa lpxa in complex with ligand L6

Analyse P. aeruginosa lpxa in complex with ligand L6 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7T5X
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: F4L
Pockets: 20 · best druggability 0.78

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

F4L · Nalpha-(tert-butoxycarbonyl)-N-1H-tetrazol-5-yl-D-tryptophanamide · ligand · 6 copies · chains A, B, C, D, F, E

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

Pockets

20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	855	0.78	0.81	93	empty
2	498	0.73	0.82	52	F4L
3	96	0.72	0.94	19	empty
4	512	0.69	0.79	60	F4L
5	601	0.69	0.78	63	F4L

Interfaces

8 interfaces between chains.

E–F · 1008 Å² buried · 9 hydrogen bonds · protein-protein
B–C · 992 Å² buried · 9 hydrogen bonds · protein-protein
A–C · 989 Å² buried · 10 hydrogen bonds · protein-protein
D–F · 973 Å² buried · 10 hydrogen bonds · protein-protein
A–B · 968 Å² buried · 11 hydrogen bonds · protein-protein

Compared structures

7T5X · P. aeruginosa LpxA in complex with ligand L6 · the same entry in another collection · chain D against D, 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 7T5X · PDBe 7T5X · UniProt A6V1E4

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