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Crystal structure of mure from E.COLI in complex with Z57299368

Analyse Crystal structure of mure from E.COLI in complex with Z57299368 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7B6L
Type: protein
Length: 965 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Udp-N-acetylmuramoyl-L-alanyl-D-glutamate-2,6- diaminopimelate ligase
EC: 6.3.2.13
UniProt: P22188
Ligands: SZK
Pockets: 20 · best druggability 0.78

Structure

x-ray diffraction · 2 distinct chains · 35% helix, 24% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Udp-N-acetylmuramoyl-L-alanyl-D-glutamate-2,6- diaminopimelate ligase (EC 6.3.2.13)	protein	487	35% helix, 24% strand	P22188
B	Udp-N-acetylmuramoyl-L-alanyl-D-glutamate-2,6- diaminopimelate ligase (EC 6.3.2.13)	protein	478	35% helix, 24% strand	P22188

Ligands and binding sites

SZK · (1-ethyl-1H-benzoimidazol-2-yl)-furan-2-ylmethyl-aminee · ligand · 2 copies · chains A, B
IPA · Isopropyl alcohol · additive · 3 copies · chains A, 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, 7 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	211	0.78	0.92	32	SZK
2	214	0.75	0.90	33	SZK
3	286	0.67	0.83	33	empty
4	263	0.66	0.83	26	IPA
5	405	0.64	0.79	31	empty

Interfaces

1 interface between chains.

A–B · 386 Å² buried · 7 hydrogen bonds · protein-protein

Compared structures

7B6L · Crystal structure of MurE from E.coli in complex with Z57299368 · the same entry in another collection · chain A against A, TM-score 1.00
P22188 · AlphaFold monomer V2.0 prediction for udp-N-acetylmuramoyl-L-alanyl… · a predicted model of the same protein · chain B against A, TM-score 0.81

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 P22188
Elsewhere: RCSB PDB 7B6L · PDBe 7B6L · UniProt P22188

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