Research workbench
Crystal structure of ampc ENT385 complex form with ceftazidime
Analyse Crystal structure of ampc ENT385 complex form with ceftazidime in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6LC9
- Type
- protein
- Length
- 670 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-lactamase
- EC
- 3.5.2.6
- Ligands
- CAZ, SO4
- Pockets
- 7 · best druggability 0.65
Structure
x-ray diffraction · 2 distinct chains · 40% 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 | 313 | 41% helix, 25% strand | — |
Ligands and binding sites
- CAZ · Acylated ceftazidime · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 6 copies · chains A, B
- DIO · 1,4-diethylene dioxide · additive · 3 copies · chains A
- GOL · Glycerol · additive · 2 copies · chains A
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 | 590 | 0.65 | 0.76 | 68 | CAZ, DIO |
| 2 | 157 | 0.46 | 0.76 | 27 | GOL |
| 3 | 71 | 0.40 | 0.80 | 20 | empty |
| 4 | 114 | 0.39 | 0.75 | 17 | empty |
| 5 | 112 | 0.38 | 0.74 | 24 | empty |
Interfaces
1 interface between chains.
- A–B · 724 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 6LC9 · Crystal structure of AmpC Ent385 complex form with ceftazidime · 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 6LC9 · PDBe 6LC9
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.