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Crystal structure of PBP3 transpeptidase domain from E. COLI

Analyse Crystal structure of PBP3 transpeptidase domain from E. COLI in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7ONO
Type: protein
Length: 406 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Peptidoglycan D,D-transpeptidase ftsi
EC: 3.4.16.4
UniProt: P0AD68
Ligands: TMO
Pockets: 2 · best druggability 0.52

Structure

x-ray diffraction · 1 distinct chain · 32% helix, 23% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Peptidoglycan D,D-transpeptidase ftsi (EC 3.4.16.4)	protein	406	32% helix, 23% strand	P0AD68

Ligands and binding sites

TMO · trimethylamine oxide · 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, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	278	0.52	0.75	35	empty
2	121	0.51	0.81	21	empty

Compared structures

7ONO · Crystal structure of PBP3 transpeptidase domain from E. coli · the same entry in another collection · chain A against A, TM-score 1.00
P0AD68 · AlphaFold monomer V2.0 prediction for peptidoglycan D,D-transpeptidase ftsi (P0AD68) · a predicted model of the same protein · chain A against A, TM-score 0.98

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 P0AD68
Elsewhere: RCSB PDB 7ONO · PDBe 7ONO · UniProt P0AD68

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