Research workbench
Crystallographic structure of a phosphonate derivative of the enterobacter cloacae P99 cephalosporinase: mechanistic interpretation of a beta-lactamase transition state analog
Analyse Crystallographic structure of a phosphonate derivative of the enterobacter… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1BLS
- Type
- protein
- Length
- 718 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-lactamase
- EC
- 3.5.2.6
- UniProt
- P05364
- Ligands
- IPP
- Pockets
- 5 · best druggability 0.64
Structure
x-ray diffraction · 1 distinct chain · 40% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Beta-lactamase (EC 3.5.2.6) | protein | 359 | 40% helix, 22% strand | P05364 |
Ligands and binding sites
- IPP · (P-iodophenylacetylamino)methylphosphinic acid · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 282 | 0.64 | 0.81 | 47 | IPP |
| 2 | 262 | 0.63 | 0.81 | 35 | IPP |
| 3 | 70 | 0.31 | 0.74 | 15 | empty |
| 4 | 52 | 0.31 | 0.76 | 25 | empty |
| 5 | 63 | 0.27 | 0.73 | 19 | empty |
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 1BLS · Crystallographic structure of a phosphonate derivative of the enterobacter cloacae P99… · 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 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 P05364
- Elsewhere: RCSB PDB 1BLS · PDBe 1BLS · UniProt P05364
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