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Crystal structure of PBP3 complexed with mc-1

Analyse Crystal structure of PBP3 complexed with mc-1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3PBT
Type: protein
Length: 501 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Penicillin-binding protein 3
UniProt: Q51504
Ligands: UE1
Pockets: 3 · best druggability 0.62

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	501	35% helix, 25% strand	Q51504

Ligands and binding sites

UE1 · (4S,7Z)-7-(2-amino-1,3-thiazol-4-yl)-1-[({4-[(2R)-2,3-dihydroxypropyl]-3-(4,5-dihydroxypyridin-2-yl)-5-oxo-4,5-dihydro- 1H-1,2,4-triazol-1-yl}sulfonyl)amino]-4-formyl-10,10-dimethyl-1,6-dioxo-9-oxa-2,5,8-triazaundec-7-en-11-oate · ligand · chains A

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

Pockets

3 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	381	0.62	0.78	36	UE1
2	202	0.54	0.78	35	empty
3	56	0.29	0.75	17	empty

Modifications

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

Compared structures

3PBT · Crystal structure of PBP3 complexed with MC-1 · 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 3PBT · PDBe 3PBT · UniProt Q51504

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