Research workbench
Crystal structure of penicillin-binding protein 3 from pseudomonas aeruginosa in complex with piperacillin
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
- 4KQO
- Type
- protein
- Length
- 1,003 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Penicillin-binding protein 3
- UniProt
- G3XD46
- Ligands
- JPP, CL
- Pockets
- 4 · best druggability 0.81
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 | 513 | 34% helix, 27% strand | G3XD46 |
| B | Penicillin-binding protein 3 | protein | 490 | 36% helix, 23% strand | G3XD46 |
Ligands and binding sites
- JPP · Piperacillin (Open Form) · ligand · 2 copies · chains A, B
- CL · Chloride ion · ion · 2 copies · chains B
- GOL · Glycerol · additive · 3 copies · chains A, B
- IMD · Imidazole · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1033 | 0.81 | 0.82 | 79 | GOL |
| 2 | 1196 | 0.78 | 0.80 | 110 | JPP |
| 3 | 388 | 0.63 | 0.78 | 37 | JPP |
| 4 | 143 | 0.42 | 0.75 | 24 | empty |
Interfaces
1 interface between chains.
- A–B · 1258 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 4KQO · 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 A against A, TM-score 0.94
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 4KQO · PDBe 4KQO · UniProt G3XD46
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