Research workbench
Crystal structure of fluorophore-labeled beta-lactamase penp in complex with cefotaxime
Analyse Crystal structure of fluorophore-labeled beta-lactamase penp in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3SH9
- Type
- protein
- Length
- 510 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-lactamase
- EC
- 3.5.2.6
- UniProt
- P00808
- Ligands
- CEF, BB0
- Pockets
- 3 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-lactamase (EC 3.5.2.6) | protein | 254 | 43% helix, 18% strand | P00808 |
| B | Beta-lactamase (EC 3.5.2.6) | protein | 256 | 41% helix, 18% strand | P00808 |
Ligands and binding sites
- CEF · CEFOTAXIME, C3' cleaved, open, bound form · ligand · 2 copies · chains A, B
- BB0 · 1-[6-(dimethylamino)naphthalen-2-yl]ethanone · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 862 | 0.75 | 0.79 | 72 | empty |
| 2 | 315 | 0.67 | 0.82 | 49 | CEF |
| 3 | 481 | 0.66 | 0.78 | 70 | CEF |
Interfaces
1 interface between chains.
- A–B · 590 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 3SH9 · Crystal structure of fluorophore-labeled beta-lactamase PenP in complex with cefotaxime · the same entry in another collection · chain A against A, TM-score 1.00
- P00808 · AlphaFold monomer V2.0 prediction for beta-lactamase (P00808) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 P00808
- Elsewhere: RCSB PDB 3SH9 · PDBe 3SH9 · UniProt P00808
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