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Crystal structure of PBP3 complexed with meropenem

Analyse Crystal structure of PBP3 complexed with meropenem in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3PBR
Type: protein
Length: 498 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Penicillin-binding protein 3
UniProt: Q51504
Ligands: MER
Pockets: 2 · best druggability 0.58

Structure

x-ray diffraction · 1 distinct chain · 35% helix, 25% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Penicillin-binding protein 3	protein	498	35% helix, 25% strand	Q51504

Ligands and binding sites

MER · (4R,5S)-3-{[(3S,5S)-5-(dimethylcarbamoyl)pyrrolidin-3-yl]sulfanyl}-5-[(2S,3R)-3-hydroxy-1-oxobutan-2-yl]-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

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	303	0.58	0.77	32	MER
2	227	0.55	0.78	36	empty

Modifications

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

Compared structures

3PBR · Crystal structure of PBP3 complexed with 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 Q51504
Elsewhere: RCSB PDB 3PBR · PDBe 3PBR · UniProt Q51504

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