Research workbench
Ctx-M-9 class a beta-lactamase complexed with compound 1 (GF4)
Analyse Ctx-M-9 class a beta-lactamase complexed with compound 1 (GF4) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3G2Y
- Type
- protein
- Length
- 524 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-lactamase ctx-M-9A
- EC
- 3.5.2.6
- UniProt
- Q9L5C8
- Ligands
- GF4
- Pockets
- 2 · best druggability 0.33
Structure
x-ray diffraction · 2 distinct chains · 44% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-lactamase ctx-M-9A (EC 3.5.2.6) | protein | 263 | 43% helix, 19% strand | Q9L5C8 |
| B | Beta-lactamase ctx-M-9A (EC 3.5.2.6) | protein | 261 | 44% helix, 20% strand | Q9L5C8 |
Ligands and binding sites
- GF4 · 4-ethyl-5-methyl-2-(1H-tetrazol-5-yl)-1,2-dihydro-3H-pyrazol-3-one · ligand · 2 copies · chains A, B
- DMS · Dimethyl sulfoxide · additive · chains 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 | 84 | 0.33 | 0.75 | 21 | GF4 |
| 2 | 85 | 0.32 | 0.74 | 20 | GF4 |
Interfaces
1 interface between chains.
- A–B · 133 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (cyclization).
Compared structures
- 3G2Y · CTX-M-9 class A beta-lactamase complexed with compound 1 (GF4) · 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 3G2Y · PDBe 3G2Y · UniProt Q9L5C8
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