Research workbench
CDD-1 beta-lactamase in imidazole/MPD 1 minute avibactam complex
Analyse CDD-1 beta-lactamase in imidazole/MPD 1 minute avibactam complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7MEA
- Type
- protein
- Length
- 250 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.73
- Source
- Clostridioides difficile
- Molecule
- Beta-lactamase
- EC
- 3.5.2.6
- UniProt
- A0A160YKM3
- Ligands
- NXL, SO4
- Pockets
- 1 · best druggability 0.40
Structure
x-ray diffraction · resolution 1.73 · 1 distinct chain · 37% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-lactamase (EC 3.5.2.6) | protein | 250 | 37% helix, 20% strand | A0A160YKM3 |
Ligands and binding sites
- NXL · (2S,5R)-1-formyl-5-[(sulfooxy)amino]piperidine-2-carboxamide · ligand · chains A
- SO4 · Sulfate ion · ion · 5 copies · chains A
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 144 | 0.40 | 0.74 | 25 | NXL, SO4 |
Modifications
Observed in the structure: 1 covalent, 1 modified (covalent ligand, carboxylation).
Compared structures
- 7MEA · Cdd-1 beta-lactamase in IMIDAZOLE/MPD 1 minute avibactam 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 A0A160YKM3
- Elsewhere: RCSB PDB 7MEA · PDBe 7MEA · UniProt A0A160YKM3
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