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NMR structure of the catalytic domain from E. faecium L,D- transpeptidase acylated by ertapenem

Analyse NMR structure of the catalytic domain from E. faecium L,D- transpeptidase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3ZGP
Type: protein
Length: 129 residues
Chains: 1
Method: solution nmr
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: ERFK/YBIS/YCFS/YNHG
EC: 2.3.2.12
UniProt: Q3Y185
Ligands: 1RG
Pockets: 1 · best druggability 0.38

Structure

solution nmr · 1 distinct chain · 5% helix, 31% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	ERFK/YBIS/YCFS/YNHG (EC 2.3.2.12)	protein	129	5% helix, 31% strand	Q3Y185

Ligands and binding sites

1RG · (4R,5S)-3-({(3S,5S)-5-[(3-carboxyphenyl) carbamoyl]pyrrolidin-3-yl}sulfanyl)-5-[(1S,2R)-1-formyl-2-hydroxypropyl]-4-methyl-4,5-dihydro-1H-pyrrole-2-carboxylic acid · ligand · chains A

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	84	0.38	0.77	23	1RG

Modifications

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

Compared structures

3ZGP · NMR structure of the catalytic domain from E. faecium L,D- transpeptidase acylated by… · 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 Q3Y185
Elsewhere: RCSB PDB 3ZGP · PDBe 3ZGP · UniProt Q3Y185

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