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Crystal structure of Pseudomonas aeruginosa penicillin-binding protein 3 (PBP3) complexed with ceftobiprole
Analyse Crystal structure of Pseudomonas aeruginosa penicillin-binding protein 3 (PBP3)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6VJE
- Type
- protein
- Length
- 502 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.76
- Source
- Pseudomonas aeruginosa
- Molecule
- Peptidoglycan D,D-transpeptidase FtsI
- EC
- 3.4.16.4
- UniProt
- Q51504
- Ligands
- RB6, CL
- Pockets
- 3 · best druggability 0.65
Structure
x-ray diffraction · resolution 1.76 · 1 distinct chain · 34% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Peptidoglycan D,D-transpeptidase FtsI (EC 3.4.16.4) | protein | 502 | 34% helix, 25% strand | Q51504 |
Ligands and binding sites
- RB6 · (2R)-2-[(1R)-1-{[(2Z)-2-(5-amino-1,2,4-thiadiazol-3-yl)-2-(hydroxyimino)acetyl]amino}-2-oxoethyl]-5-({2-oxo-1-[(3R)-pyr rolidin-3-yl]-2,5-dihydro-1H-pyrrol-3-yl}methyl)-3,6-dihydro-2H-1,3-thiazine-4-carboxylic acid · ligand · chains A
- CL · Chloride ion · ion · 2 copies · 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.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 446 | 0.65 | 0.78 | 45 | RB6, CL |
| 2 | 328 | 0.56 | 0.75 | 46 | empty |
| 3 | 50 | 0.25 | 0.74 | 15 | empty |
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 6VJE · Crystal structure of pseudomonas aeruginosa penicillin-binding protein 3 (PBP3) complexed… · 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 6VJE · PDBe 6VJE · UniProt Q51504
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