Research workbench
Crystal structure of S02030 boronic acid inhibitor complexed to shv-1 beta-lactamase
Analyse Crystal structure of S02030 boronic acid inhibitor complexed to shv-1… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5EE8
- Type
- protein
- Length
- 265 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-lactamase shv-1
- EC
- 3.5.2.6
- UniProt
- P0AD64
- Ligands
- MA4, ZXM
- Pockets
- 2 · best druggability 0.68
Structure
x-ray diffraction · 1 distinct chain · 46% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-lactamase shv-1 (EC 3.5.2.6) | protein | 265 | 46% helix, 17% strand | P0AD64 |
Ligands and binding sites
- MA4 · Cyclohexyl-hexyl-beta-D-maltoside · ligand · 2 copies · chains A
- ZXM · 1-{(2R)-2-(dihydroxyboranyl)-2-[(thiophen-2-ylacetyl) amino]ethyl}-1H-1,2,3-triazole-4-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 | 203 | 0.68 | 0.86 | 24 | empty |
| 2 | 54 | 0.26 | 0.74 | 16 | ZXM |
Modifications
Observed in the structure: 1 covalent, 1 disulfide (covalent ligand, disulfide).
Compared structures
- 5EE8 · Crystal structure of S02030 boronic acid inhibitor complexed to SHV-1 beta-lactamase · the same entry in another collection · chain A against A, TM-score 1.00
- P0AD64 · AlphaFold monomer V2.0 prediction for beta-lactamase shv-1 (P0AD64) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 P0AD64
- Elsewhere: RCSB PDB 5EE8 · PDBe 5EE8 · UniProt P0AD64
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