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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
- 4KQR
- Type
- protein
- Length
- 1,038 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.01
- Source
- Pseudomonas aeruginosa
- Molecule
- Penicillin-binding protein 3
- UniProt
- G3XD46
- Ligands
- VPP, CL
- Pockets
- 6 · best druggability 0.81
Structure
x-ray diffraction · resolution 2.01 · 2 distinct chains · 34% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Penicillin-binding protein 3 | protein | 520 | 34% helix, 26% strand | G3XD46 |
| B | Penicillin-binding protein 3 | protein | 518 | 34% helix, 26% 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 · 5 copies · chains A, B
- GOL · Glycerol · additive · 9 copies · chains A, B
- IMD · Imidazole · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1195 | 0.81 | 0.82 | 84 | CL, GOL |
| 2 | 760 | 0.76 | 0.81 | 67 | VPP |
| 3 | 344 | 0.63 | 0.79 | 42 | VPP, IMD |
| 4 | 252 | 0.57 | 0.78 | 42 | empty |
| 5 | 310 | 0.56 | 0.76 | 48 | empty |
Interfaces
1 interface between chains.
- A–B · 1308 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 4KQR · 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 0.92
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 4KQR · PDBe 4KQR · UniProt G3XD46
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