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Crystal structure of E. coli PBP5-meropenem

Analyse Crystal structure of E. coli PBP5-meropenem in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6NTZ
Type: protein
Length: 367 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 2.2
Source: Escherichia coli
Molecule: D-alanyl-D-alanine carboxypeptidase
EC: 3.4.16.4
UniProt: A0A0A0GRC5
Ligands: MXR
Pockets: 2 · best druggability 0.42

Structure

x-ray diffraction · resolution 2.2 · 1 distinct chain · 31% helix, 31% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	D-alanyl-D-alanine carboxypeptidase (EC 3.4.16.4)	protein	367	31% helix, 31% strand	A0A0A0GRC5

Ligands and binding sites

MXR · (2S,3R,4S)-4-{[(3S,5R)-5-(dimethylcarbamoyl)pyrrolidin-3-yl]sulfanyl}-2-[(2S,3R)-3-hydroxy-1-oxobutan-2-yl]-3-methyl-3,4-dihydro-2H-pyrrole-5-carboxylic acid · ligand · chains A

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

Pockets

2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	135	0.42	0.75	27	MXR
2	98	0.37	0.75	24	empty

Modifications

Observed in the structure: 1 covalent (covalent ligand).

Compared structures

6NTZ · Crystal structure of E. COLI PBP5-meropenem · 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 A0A0A0GRC5
Elsewhere: RCSB PDB 6NTZ · PDBe 6NTZ · UniProt A0A0A0GRC5

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