Research workbench
Crystal Structure of a Class D carbapenemase complexed with Avibactam
Analyse Crystal Structure of a Class D carbapenemase complexed with Avibactam in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7O5N
- Type
- protein
- Length
- 969 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.6
- Source
- Klebsiella pneumoniae
- Molecule
- Beta-lactamase
- EC
- 3.5.2.6
- UniProt
- Q6XEC0
- Ligands
- NXL, CL
- Pockets
- 8 · best druggability 0.78
Structure
x-ray diffraction · resolution 1.6 · 2 distinct chains · 41% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| AAA | Beta-lactamase (EC 3.5.2.6) | protein | 243 | 40% helix, 21% strand | Q6XEC0 |
| BBB, CCC, DDD | Beta-lactamase (EC 3.5.2.6) | protein | 242 | 41% helix, 21% strand | Q6XEC0 |
Ligands and binding sites
- NXL · (2S,5R)-1-formyl-5-[(sulfooxy)amino]piperidine-2-carboxamide · ligand · 4 copies · chains AAA, BBB, CCC, DDD
- CL · Chloride ion · ion · 8 copies · chains AAA, BBB, CCC, DDD
- 1BO · 1-butanol · additive · 5 copies · chains AAA, BBB, CCC
- GOL · Glycerol · additive · 3 copies · chains BBB, CCC, DDD
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 966 | 0.78 | 0.80 | 122 | NXL, CL |
| 2 | 939 | 0.78 | 0.80 | 127 | NXL, CL |
| 3 | 166 | 0.47 | 0.76 | 26 | empty |
| 4 | 197 | 0.46 | 0.74 | 26 | empty |
| 5 | 59 | 0.36 | 0.79 | 18 | 1BO |
Interfaces
4 interfaces between chains.
- CCC–DDD · 974 Ų buried · 18 hydrogen bonds · protein-protein
- AAA–BBB · 962 Ų buried · 18 hydrogen bonds · protein-protein
- BBB–DDD · 305 Ų buried · 3 hydrogen bonds · protein-protein
- AAA–CCC · 188 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent (covalent ligand).
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 7O5N · PDBe 7O5N · UniProt Q6XEC0
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