Research workbench
OXA-48_P68A-CAZ. Evolutionary trade-offs of OXA-48 mediated ceftazidime-avibactam resistance
Analyse OXA-48_P68A-CAZ. Evolutionary trade-offs of OXA-48 mediated… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6Q5F
- Type
- protein
- Length
- 942 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.5
- Source
- Klebsiella pneumoniae
- Molecule
- Beta-lactamase
- EC
- 3.5.2.6
- UniProt
- Q6XEC0
- Ligands
- CTJ, CL, SO4
- Pockets
- 9 · best druggability 0.78
Structure
x-ray diffraction · resolution 2.5 · 2 distinct chains · 41% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Beta-lactamase (EC 3.5.2.6) | protein | 229 | 42% helix, 24% strand | Q6XEC0 |
| B, D | Beta-lactamase (EC 3.5.2.6) | protein | 242 | 40% helix, 19% strand | Q6XEC0 |
Ligands and binding sites
- CTJ · 1-({(2R)-2-[(1R)-1-{[(2Z)-2-(2-amino-1,3-thiazol-4-yl)-2-{[(2-carboxypropan-2-yl)oxy]imino}acetyl]amino}-2-oxoethyl]-4-carboxy-3,6-dihydro-2H-1,3-thiazin-5-yl}methyl)pyridinium · ligand · 2 copies · chains A, C
- CL · Chloride ion · ion · 6 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · chains D
- PGE · Triethylene glycol · additive · 3 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 810 | 0.78 | 0.82 | 109 | CL |
| 2 | 690 | 0.78 | 0.83 | 92 | CL |
| 3 | 143 | 0.43 | 0.75 | 20 | empty |
| 4 | 120 | 0.40 | 0.74 | 16 | empty |
| 5 | 62 | 0.39 | 0.80 | 16 | empty |
Interfaces
3 interfaces between chains.
- C–D · 1002 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 969 Ų buried · 19 hydrogen bonds · protein-protein
- A–C · 101 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 2 covalent, 2 modified (covalent ligand, carboxylation).
Compared structures
- 6Q5F · Oxa-48_P68A-caz. evolutionary trade-offs of oxa-48 mediated ceftazidime-avibactam… · 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 Q6XEC0
- Elsewhere: RCSB PDB 6Q5F · PDBe 6Q5F · UniProt Q6XEC0
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