MolNFT v1 · #169365 · protein

Pseudomonas aeruginosa murc with AZ5595

6X9N · Udp-N-acetylmuramate--L-alanine ligase: “Pseudomonas aeruginosa murc with AZ5595”. X-ray diffraction, 3 ligands (UYD, VAL, CL), 20 pockets (best druggability 0.59). MolNFT v1 #169365 on GenesisL1: 3D structure, binding sites and…

PDB: 6X9N
Type: protein
Length: 2,439 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: UYD, VAL, CL
Pockets: 20 · best druggability 0.59

Structure

x-ray diffraction · 2 distinct chains · 35% helix, 25% strand (DSSP).

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

Ligands and binding sites

UYD · (2R)-2-({4-[(5-tert-butyl-1-methyl-1H-pyrazol-3-yl) amino]-1H-pyrazolo[3,4-d]pyrimidin-6-yl}amino)-2-phenylethan-1-ol · ligand · 8 copies · chains A, B, C, D, E, F, G, H
VAL · Valine · ligand · chains H
CL · Chloride ion · ion · 8 copies · chains A, G, B, E, C, D, F, H
EDO · 1,2-ethanediol · additive · 34 copies · chains A, G, B, E, C, D, F, H
DMS · Dimethyl sulfoxide · additive · 14 copies · chains A, B, E, C, D, 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	88	0.59	0.87	20	empty
2	89	0.58	0.87	18	empty
3	105	0.58	0.85	17	empty
4	135	0.58	0.84	31	EDO
5	94	0.57	0.86	19	empty

Interfaces

10 interfaces between chains.

B–E · 1297 Å² buried · 18 hydrogen bonds · protein-protein
C–D · 1290 Å² buried · 15 hydrogen bonds · protein-protein
A–G · 1284 Å² buried · 17 hydrogen bonds · protein-protein
F–H · 1280 Å² buried · 16 hydrogen bonds · protein-protein
C–E · 676 Å² buried · 10 hydrogen bonds · protein-protein

Compared structures

6X9N · Pseudomonas aeruginosa MurC with AZ5595 · 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 G 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 6X9N · PDBe 6X9N · UniProt Q9HW02

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