Research workbench

Crystal structure of pseudomonas aeruginosa lpxa in complex with compound 45

Analyse Crystal structure of pseudomonas aeruginosa lpxa in complex with compound 45 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7OKB
Type: protein
Length: 7,725 residues
Chains: 30
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: A0A069Q726
Ligands: VFZ, SO4, CL
Pockets: 20 · best druggability 0.76

Structure

x-ray diffraction · 2 distinct chains · 17% helix, 29% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F, J, K, L, S, T, U, Y, Z, c	Acyl-[acyl-carrier-protein]--udp-N-acetylglucosamine O- acyltransferase (EC 2.3.1.129)	protein	258	17% helix, 29% strand	A0A069Q726
G, H, I, M, N, O, P, Q, R, V, W, X, a, b, d	Acyl-[acyl-carrier-protein]--udp-N-acetylglucosamine O- acyltransferase (EC 2.3.1.129)	protein	257	17% helix, 28% strand	A0A069Q726

Ligands and binding sites

VFZ · ~{N}-[(5-azanyl-1,3,4-oxadiazol-2-yl)methyl]-2-(2-chlorophenyl)sulfanyl-~{N}-[(6-oxidanylidene-1~{H}-pyridin-3-yl)methyl]ethanamide · ligand · 30 copies · chains A, B, C, D, E, F, G, H, I, M, N, O, J, K, L, P, Q, R, S, T, U, V, W, X, Y, Z, a, b, c, d
SO4 · Sulfate ion · ion · 54 copies · chains A, B, C, D, E, F, G, H, I, M, N, O, J, K, L, P, Q, R, S, T, U, V, W, X, Y, Z, a, b, c, d
CL · Chloride ion · ion · 26 copies · chains A, B, C, D, E, G, I, M, N, O, L, Q, S, T, X

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1034	0.76	0.78	91	CL, SO4, VFZ
2	922	0.75	0.78	94	SO4, VFZ
3	91	0.74	0.96	19	empty
4	93	0.74	0.96	20	empty
5	895	0.74	0.78	98	CL, SO4, VFZ

Interfaces

66 interfaces between chains.

A–a · 1241 Å² buried · 29 hydrogen bonds · protein-protein
K–R · 1230 Å² buried · 27 hydrogen bonds · protein-protein
E–I · 1222 Å² buried · 26 hydrogen bonds · protein-protein
T–X · 1214 Å² buried · 28 hydrogen bonds · protein-protein
F–P · 1209 Å² buried · 27 hydrogen bonds · protein-protein

Compared structures

7OKB · Crystal structure of Pseudomonas aeruginosa LpxA in complex with compound 45 · 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 A0A069Q726
Elsewhere: RCSB PDB 7OKB · PDBe 7OKB · UniProt A0A069Q726

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