MolNFT v1 · #116469 · protein

Structure of pseudomonas aeruginosa lpxa

5DEM · Acyl-[acyl-carrier-protein]--udp-N-acetylglucosamine O…: “Structure of pseudomonas aeruginosa lpxa”. X-ray diffraction, 1 ligand (PO4), 20 pockets (best druggability 0.77). MolNFT v1 #116469 on GenesisL1: 3D structure, binding sites…

PDB: 5DEM
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: PO4
Pockets: 20 · best druggability 0.77

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

PO4 · Phosphate ion · ion · chains B

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	617	0.77	0.83	84	empty
2	300	0.74	0.86	55	empty
3	77	0.72	0.96	18	empty
4	81	0.72	0.95	17	empty
5	574	0.70	0.79	71	empty

Interfaces

8 interfaces between chains.

E–F · 1031 Å² buried · 13 hydrogen bonds · protein-protein
B–C · 1028 Å² buried · 10 hydrogen bonds · protein-protein
A–C · 1006 Å² buried · 11 hydrogen bonds · protein-protein
A–B · 1005 Å² buried · 11 hydrogen bonds · protein-protein
D–E · 1004 Å² buried · 9 hydrogen bonds · protein-protein

Compared structures

5DEM · Structure of Pseudomonas aeruginosa LpxA · 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 5DEM · PDBe 5DEM · UniProt A6V1E4

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