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Crystal structure of penicillin-binding protein 3 from pseudomonas aeruginosa in complex with (5S)-penicilloic acid

Analyse Crystal structure of penicillin-binding protein 3 from pseudomonas aeruginosa… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4KQQ
Type: protein
Length: 1,019 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Penicillin-binding protein 3
UniProt: G3XD46
Ligands: VPP, CL
Pockets: 6 · best druggability 0.84

Structure

x-ray diffraction · 2 distinct chains · 35% helix, 25% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Penicillin-binding protein 3	protein	520	34% helix, 27% strand	G3XD46
B	Penicillin-binding protein 3	protein	499	35% helix, 23% strand	G3XD46

Ligands and binding sites

VPP · (2S,4S)-2-[(R)-carboxy{[(2R)-2-{[(4-ethyl-2,3-dioxopiperazin-1-yl)carbonyl]amino}-2-phenylacetyl]amino}methyl]-5,5-dimethyl-1,3-thiazolidine-4-carboxylic acid · ligand · 2 copies · chains A, B
CL · Chloride ion · ion · 3 copies · chains A, B
GOL · Glycerol · additive · 5 copies · chains A, B
IMD · Imidazole · additive · chains A

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

Pockets

6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1005	0.84	0.84	80	GOL
2	1080	0.78	0.80	97	VPP
3	339	0.64	0.79	41	VPP, IMD
4	98	0.44	0.79	22	empty
5	125	0.41	0.76	18	empty

Interfaces

1 interface between chains.

A–B · 1325 Å² buried · 19 hydrogen bonds · protein-protein

Compared structures

4KQQ · CRYSTAL STRUCTURE OF PENICILLIN-BINDING PROTEIN 3 FROM PSEUDOMONAS AERUGINOSA IN COMPLEX… · the same entry in another collection · chain A against A, TM-score 1.00
G3XD46 · AlphaFold monomer V2.0 prediction for peptidoglycan D,D-transpeptidase ftsi (G3XD46) · a predicted model of the same protein · chain B against A, TM-score 0.93

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 G3XD46
Elsewhere: RCSB PDB 4KQQ · PDBe 4KQQ · UniProt G3XD46

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