Research workbench
Ctx-M-9 class a beta-lactamase complexed with compound 18
Analyse Ctx-M-9 class a beta-lactamase complexed with compound 18 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4DE1
- Type
- protein
- Length
- 524 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-lactamase
- EC
- 3.5.2.6
- UniProt
- Q9L5C8
- Ligands
- 0J6
- Pockets
- 2 · best druggability 0.35
Structure
x-ray diffraction · 2 distinct chains · 44% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-lactamase (EC 3.5.2.6) | protein | 263 | 43% helix, 19% strand | Q9L5C8 |
| B | Beta-lactamase (EC 3.5.2.6) | protein | 261 | 44% helix, 20% strand | Q9L5C8 |
Ligands and binding sites
- 0J6 · N-[3-(1H-tetrazol-5-yl)phenyl]-2H-indazole-5-carboxamide · ligand · 3 copies · chains A, B
- DMS · Dimethyl sulfoxide · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 97 | 0.35 | 0.75 | 21 | 0J6 |
| 2 | 74 | 0.31 | 0.75 | 20 | 0J6 |
Interfaces
1 interface between chains.
- A–B · 129 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 1 modified (cyclization).
Compared structures
- 4DE1 · CTX-M-9 class A beta-lactamase complexed with compound 18 · 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 Q9L5C8
- Elsewhere: RCSB PDB 4DE1 · PDBe 4DE1 · UniProt Q9L5C8
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.