MolNFT v1 · #84485 · protein

Crystal structure of murf ligase in complex with cyanothiophene inhibitor

3ZM5 · Udp-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase: “Crystal structure of murf ligase in complex with cyanothiophene inhibitor”. X-ray diffraction, 1 ligand (IGM), 4 pockets (best druggability 0.83). MolNFT v1 #84485 on…

PDB: 3ZM5
Type: protein
Length: 454 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Udp-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase
EC: 6.3.2.10
UniProt: Q8DNV6
Ligands: IGM
Pockets: 4 · best druggability 0.83

Structure

x-ray diffraction · 1 distinct chain · 36% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Udp-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase (EC 6.3.2.10)	protein	454	36% helix, 19% strand	Q8DNV6

Ligands and binding sites

IGM · 2,4-bis(chloranyl)-N-[3-cyano-6-[(4-hydroxyphenyl)methyl]-5,7-dihydro-4H-thieno[2,3-c]pyridin-2-yl]-5-morpholin-4-ylsulfonyl-benzamide · ligand · chains A

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1112	0.83	0.84	77	IGM
2	103	0.47	0.80	19	empty
3	52	0.36	0.80	14	empty
4	86	0.34	0.74	17	empty

Compared structures

3ZM5 · Crystal structure of murf ligase in complex with cyanothiophene inhibitor · 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 Q8DNV6
Elsewhere: RCSB PDB 3ZM5 · PDBe 3ZM5 · UniProt Q8DNV6

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