MolNFT v1 · #167122 · protein

Crystal structure of transpeptidase domain of PBP2 from neisseria gonorrhoeae cephalosporin-resistant strain H041 acylated by ceftriaxone

6VBD · Probable peptidoglycan D,D-transpeptidase pena: “Crystal structure of transpeptidase domain of PBP2 from neisseria gonorrhoeae cephalosporin-resistant strain…”. X-ray diffraction, 1 ligand (CEF), 1 pocket (best druggability 0.48).…

PDB: 6VBD
Type: protein
Length: 324 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Probable peptidoglycan D,D-transpeptidase pena
EC: 3.4.16.4
UniProt: F2Z7K9
Ligands: CEF
Pockets: 1 · best druggability 0.48

Structure

x-ray diffraction · 1 distinct chain · 37% helix, 23% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Probable peptidoglycan D,D-transpeptidase pena (EC 3.4.16.4)	protein	324	37% helix, 23% strand	F2Z7K9

Ligands and binding sites

CEF · CEFOTAXIME, C3' cleaved, open, bound form · ligand · chains A
GOL · Glycerol · additive · 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	203	0.48	0.75	34	CEF

Modifications

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

Compared structures

6VBD · Crystal structure of transpeptidase domain of PBP2 from Neisseria gonorrhoeae… · 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 F2Z7K9
Elsewhere: RCSB PDB 6VBD · PDBe 6VBD · UniProt F2Z7K9

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