MolNFT v1 · #179744 · protein
Avibactam-cdd-1 45 minute complex
7KER · Beta-lactamase: “Avibactam-cdd-1 45 minute complex”. X-ray diffraction, 3 ligands (NXL, FYG, SO4), 1 pocket (best druggability 0.42). MolNFT v1 #179744 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7KER
- Type
- protein
- Length
- 251 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-lactamase
- EC
- 3.5.2.6
- UniProt
- A0A160YKM3
- Ligands
- NXL, FYG, SO4
- Pockets
- 1 · best druggability 0.42
Structure
x-ray diffraction · 1 distinct chain · 37% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-lactamase (EC 3.5.2.6) | protein | 251 | 37% helix, 20% strand | A0A160YKM3 |
Ligands and binding sites
- NXL · (2S,5R)-1-formyl-5-[(sulfooxy)amino]piperidine-2-carboxamide · ligand · chains A
- FYG · (2S,5R)-7-oxo-6-(sulfooxy)-1,6-diazabicyclo[3.2.1]octane-2-carboxamide · ligand · chains A
- SO4 · Sulfate ion · ion · 5 copies · chains A
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · 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 | 157 | 0.42 | 0.74 | 26 | NXL, EPE |
Modifications
Observed in the structure: 1 covalent, 1 modified (covalent ligand, carboxylation).
Compared structures
- 7KER · avibactam-CDD-1 45 minute 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 7KER · PDBe 7KER · UniProt A0A160YKM3
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