Research workbench
Crystal structure of AmpC Ent385 complex form with avibactam
Analyse Crystal structure of AmpC Ent385 complex form with avibactam in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6LC8
- Type
- protein
- Length
- 675 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.6
- Source
- Enterobacter cloacae
- Molecule
- Beta-lactamase
- EC
- 3.5.2.6
- Ligands
- NXL, SO4
- Pockets
- 7 · best druggability 0.65
Structure
x-ray diffraction · resolution 1.6 · 2 distinct chains · 39% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-lactamase (EC 3.5.2.6) | protein | 357 | 38% helix, 23% strand | — |
| B | Beta-lactamase (EC 3.5.2.6) | protein | 318 | 41% helix, 25% strand | — |
Ligands and binding sites
- NXL · (2S,5R)-1-formyl-5-[(sulfooxy)amino]piperidine-2-carboxamide · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 11 copies · chains A, B
- DIO · 1,4-diethylene dioxide · additive · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 576 | 0.65 | 0.76 | 73 | NXL, SO4 |
| 2 | 149 | 0.44 | 0.75 | 27 | empty |
| 3 | 122 | 0.38 | 0.74 | 32 | DIO |
| 4 | 65 | 0.38 | 0.79 | 16 | empty |
| 5 | 70 | 0.33 | 0.75 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 708 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 6LC8 · Crystal structure of ampc ENT385 complex form with 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
- Elsewhere: RCSB PDB 6LC8 · PDBe 6LC8
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