Research workbench
Crystal structure of PBP2a from MRSA in complex with piperacillin and quinazoli
Analyse Crystal structure of PBP2a from MRSA in complex with piperacillin and quinazoli in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6Q9N
- Type
- protein
- Length
- 1,275 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.5
- Source
- Staphylococcus aureus (strain Mu50 / ATCC 700699)
- Molecule
- Penicillin binding protein 2 prime
- UniProt
- A0A0H3JPA5
- Ligands
- QLN, JPP, MUR, CD, CL
- Pockets
- 15 · best druggability 0.78
Structure
x-ray diffraction · resolution 2.5 · 2 distinct chains · 34% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Penicillin binding protein 2 prime | protein | 638 | 35% helix, 27% strand | A0A0H3JPA5 |
| B | Penicillin binding protein 2 prime | protein | 637 | 34% helix, 26% strand | A0A0H3JPA5 |
Ligands and binding sites
- QLN · 3-[2-[(~{E})-2-(4-ethynylphenyl)ethenyl]-4-oxidanylidene-quinazolin-3-yl]benzoic acid · ligand · chains A, B
- JPP · Piperacillin (Open Form) · ligand · chains A
- MUR · beta-muramic acid · sugar · chains A
- CD · Cadmium ion · metal · 4 copies · chains A, B
- CL · Chloride ion · ion · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1075 | 0.78 | 0.80 | 103 | CL, MUR |
| 2 | 393 | 0.63 | 0.78 | 53 | empty |
| 3 | 392 | 0.60 | 0.76 | 34 | empty |
| 4 | 350 | 0.60 | 0.77 | 36 | empty |
| 5 | 262 | 0.56 | 0.78 | 26 | JPP |
Interfaces
1 interface between chains.
- A–B · 1684 Ų buried · 27 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 6Q9N · Crystal structure of PBP2A from mrsa in complex with piperacillin and quinazolinone · 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 A0A0H3JPA5
- Elsewhere: RCSB PDB 6Q9N · PDBe 6Q9N · UniProt A0A0H3JPA5
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