Research workbench
X-ray crystal structure of ruthenocenyl-7-aminocephalosporanic acid covalent acyl-enzyme complex with ctx-M-14 E166A beta-lactamase
Analyse X-ray crystal structure of ruthenocenyl-7-aminocephalosporanic acid covalent… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6VNU
- Type
- protein
- Length
- 523 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-lactamase
- EC
- 3.5.2.6
- UniProt
- A0A1B3B7F6
- Ligands
- 7G4, TDJ, K
- Pockets
- 2 · best druggability 0.33
Structure
x-ray diffraction · 2 distinct chains · 44% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-lactamase (EC 3.5.2.6) | protein | 263 | 43% helix, 19% strand | A0A1B3B7F6 |
| B | Beta-lactamase (EC 3.5.2.6) | protein | 260 | 44% helix, 20% strand | A0A1B3B7F6 |
Ligands and binding sites
- 7G4 · ruthenocene · ligand · 3 copies · chains A, B
- TDJ · [(1,2,3,4,5-eta)-1-(4-{[carboxy(4-carboxy-5-methylidene-5,6-dihydro-2H-1,3-thiazin-2-yl) methyl]amino}-4-oxobutanoyl)cyclopentadienyl][(1,2,3, 4,5-eta)-cyclopentadienyl]ruthenium · ligand · 2 copies · chains A, B
- K · Potassium ion · metal · 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 | 70 | 0.33 | 0.76 | 21 | TDJ |
| 2 | 71 | 0.31 | 0.75 | 18 | TDJ |
Interfaces
1 interface between chains.
- A–B · 106 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 6VNU · X-ray Crystal Structure of Ruthenocenyl-7-Aminocephalosporanic Acid Covalent Acyl-Enzyme… · 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 A0A1B3B7F6
- Elsewhere: RCSB PDB 6VNU · PDBe 6VNU · UniProt A0A1B3B7F6
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