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Pseudomonas aeruginosa murc with AZ8074

Analyse Pseudomonas aeruginosa murc with AZ8074 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6X9F
Type: protein
Length: 2,434 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Udp-N-acetylmuramate--L-alanine ligase
EC: 6.3.2.8
UniProt: Q9HW02
Ligands: UXP, CL
Pockets: 20 · best druggability 0.61

Structure

x-ray diffraction · 2 distinct chains · 36% helix, 25% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, D, E, G, H	Udp-N-acetylmuramate--L-alanine ligase (EC 6.3.2.8)	protein	304	36% helix, 25% strand	Q9HW02
C, F	Udp-N-acetylmuramate--L-alanine ligase (EC 6.3.2.8)	protein	305	35% helix, 25% strand	Q9HW02

Ligands and binding sites

UXP · [(2R)-1-{4-[(5-cyclopropyl-1H-pyrazol-3-yl)amino]-2H-pyrazolo[3,4-d]pyrimidin-6-yl}piperidin-2-yl]methanol · ligand · 8 copies · chains A, B, C, D, E, F, G, H
CL · Chloride ion · ion · 5 copies · chains C, D, B, E, F, H, A, G
EDO · 1,2-ethanediol · additive · 32 copies · chains A, G, B, E, C, D, F, H
DMS · Dimethyl sulfoxide · additive · 13 copies · chains A, B, E, D, C, F, G, H

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

Pockets

20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	103	0.61	0.87	21	empty
2	133	0.59	0.85	30	EDO
3	99	0.58	0.86	19	empty
4	106	0.58	0.85	17	empty
5	102	0.58	0.85	20	empty

Interfaces

10 interfaces between chains.

F–H · 1333 Å² buried · 19 hydrogen bonds · protein-protein
B–E · 1319 Å² buried · 20 hydrogen bonds · protein-protein
A–G · 1303 Å² buried · 17 hydrogen bonds · protein-protein
C–D · 1300 Å² buried · 14 hydrogen bonds · protein-protein
C–E · 695 Å² buried · 10 hydrogen bonds · protein-protein

Compared structures

6X9F · Pseudomonas aeruginosa MurC with AZ8074 · the same entry in another collection · chain H against H, TM-score 1.00
Q9HW02 · AlphaFold monomer V2.0 prediction for udp-N-acetylmuramate--L-alanine ligase (Q9HW02) · a predicted model of the same protein · chain C against A, TM-score 0.87

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 Q9HW02
Elsewhere: RCSB PDB 6X9F · PDBe 6X9F · UniProt Q9HW02

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