Research workbench
Crystal structure of the native class C beta-lactamase from enterobacter cloacae 908R complexed with BRL42715
Analyse Crystal structure of the native class C beta-lactamase from enterobacter… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1Y54
- Type
- protein
- Length
- 359 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-lactamase
- EC
- 3.5.2.6
- UniProt
- P05364
- Ligands
- FDT
- Pockets
- 2 · best druggability 0.66
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-lactamase (EC 3.5.2.6) | protein | 359 | 39% helix, 22% strand | P05364 |
Ligands and binding sites
- FDT · (7R)-6-formyl-7-(1-methyl-1H-1,2,3-triazol-4-yl)-4,7-dihydro-1,4-thiazepine-3-carboxylic acid · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 313 | 0.66 | 0.81 | 45 | FDT |
| 2 | 83 | 0.33 | 0.74 | 19 | empty |
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 1Y54 · Crystal structure of the native class C beta-lactamase from Enterobacter cloacae 908R… · the same entry in another collection · chain A against A, TM-score 1.00
- P05364 · AlphaFold monomer V2.0 prediction for beta-lactamase (P05364) · 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 P05364
- Elsewhere: RCSB PDB 1Y54 · PDBe 1Y54 · UniProt P05364
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.