Research workbench
Crystal structure of the oxa-48 carbapenem-hydrolyzing class D beta- lactamase in complex with the dbo inhibitor ANT3310
Analyse Crystal structure of the oxa-48 carbapenem-hydrolyzing class D beta- lactamase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6ZXI
- Type
- protein
- Length
- 485 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-lactamase
- EC
- 3.5.2.6
- UniProt
- Q6XEC0
- Ligands
- QS8, CO2, CL
- Pockets
- 3 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-lactamase (EC 3.5.2.6) | protein | 243 | 40% helix, 21% strand | Q6XEC0 |
| B | Beta-lactamase (EC 3.5.2.6) | protein | 242 | 40% helix, 21% strand | Q6XEC0 |
Ligands and binding sites
- QS8 · [[(3~{R},6~{R})-6-fluoranyl-1-methanoyl-piperidin-3-yl]amino] hydrogen sulfate · ligand · 2 copies · chains A, B
- CO2 · Carbon dioxide · ion · chains A
- CL · Chloride ion · ion · chains A, B
- EDO · 1,2-ethanediol · additive · 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 879 | 0.78 | 0.81 | 128 | QS8, CO2, CL |
| 2 | 58 | 0.36 | 0.79 | 16 | empty |
| 3 | 53 | 0.35 | 0.79 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 1023 Ų buried · 21 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 6ZXI · Crystal Structure of the OXA-48 Carbapenem-Hydrolyzing Class D beta-Lactamase in Complex… · 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 6ZXI · PDBe 6ZXI · UniProt Q6XEC0
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