Research workbench
Crystal structure of beta-lactamase penp mutant-E166Y in complex with cephaloridine as "post-acylation" intermediate
Analyse Crystal structure of beta-lactamase penp mutant-E166Y 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
- 5ZG6
- Type
- protein
- Length
- 512 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
- CED
- Pockets
- 4 · best druggability 0.73
Structure
x-ray diffraction · 1 distinct chain · 45% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, A | Beta-lactamase (EC 3.5.2.6) | protein | 256 | 45% helix, 18% strand | P00808 |
Ligands and binding sites
- CED · 5-methyl-2-[2-oxo-1-(2-thiophen-2-yl-acetylamino)-ethyl]-3,6-dihydro-2H-[1,3]thiazine-4-carboxylic acid · ligand · 2 copies · chains B, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1178 | 0.73 | 0.77 | 99 | CED |
| 2 | 73 | 0.47 | 0.83 | 17 | empty |
| 3 | 74 | 0.41 | 0.80 | 18 | empty |
| 4 | 51 | 0.24 | 0.73 | 15 | CED |
Interfaces
1 interface between chains.
- B–A · 620 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 5ZG6 · Crystal structure of beta-lactamase PenP mutant-E166Y in complex with cephaloridine as… · the same entry in another collection · chain B against B, 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 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 P00808
- Elsewhere: RCSB PDB 5ZG6 · PDBe 5ZG6 · UniProt P00808
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