MolNFT v1 · #137677 · protein

Structure of murc from pseudomonas aeruginosa

5VVW · Udp-N-acetylmuramate--L-alanine ligase: “Structure of murc from pseudomonas aeruginosa”. X-ray diffraction, 20 pockets (best druggability 0.59). MolNFT v1 #137677 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5VVW
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
Pockets: 20 · best druggability 0.59

Structure

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

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

Ligands and binding sites

EDO · 1,2-ethanediol · additive · 7 copies · chains A, B, C, 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	91	0.59	0.87	19	empty
2	169	0.59	0.83	43	EDO
3	96	0.58	0.86	19	empty
4	109	0.58	0.85	21	empty
5	98	0.58	0.86	18	empty

Interfaces

10 interfaces between chains.

F–H · 1333 Å² buried · 21 hydrogen bonds · protein-protein
A–G · 1318 Å² buried · 18 hydrogen bonds · protein-protein
C–D · 1307 Å² buried · 16 hydrogen bonds · protein-protein
B–E · 1291 Å² buried · 17 hydrogen bonds · protein-protein
C–E · 693 Å² buried · 11 hydrogen bonds · protein-protein

Compared structures

5VVW · Structure of MurC from Pseudomonas aeruginosa · 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 A 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 5VVW · PDBe 5VVW · UniProt Q9HW02

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