MolNFT v1 · #74950 · protein

Crystal structure of PBP3 complexed with imipenem

3PBQ · Penicillin-binding protein 3: “Crystal structure of PBP3 complexed with imipenem”. X-ray diffraction, 1 ligand (IM2), 2 pockets (best druggability 0.58). MolNFT v1 #74950 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 3PBQ
Type: protein
Length: 493 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Penicillin-binding protein 3
UniProt: Q51504
Ligands: IM2
Pockets: 2 · best druggability 0.58

Structure

x-ray diffraction · 1 distinct chain · 34% helix, 24% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Penicillin-binding protein 3	protein	493	34% helix, 24% strand	Q51504

Ligands and binding sites

IM2 · (5R)-5-[(1S,2R)-1-formyl-2-hydroxypropyl]-3-[(2-{[(E)-iminomethyl]amino}ethyl)sulfanyl]-4,5-dihydro-1H-pyrrole-2-carbox ylic 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	231	0.58	0.79	36	IM2
2	232	0.55	0.78	37	empty

Modifications

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

Compared structures

3PBQ · Crystal structure of PBP3 complexed with imipenem · 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 3PBQ · PDBe 3PBQ · UniProt Q51504

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