Research workbench
Crystal structure of kpc-2 beta-lactamase in complex with the S02030 boronic acid inhibitor
Analyse Crystal structure of kpc-2 beta-lactamase in complex with the S02030 boronic… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5EEC
- Type
- protein
- Length
- 530 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Carbapenem-hydrolyzing beta-lactamase kpc
- EC
- 3.5.2.6
- UniProt
- Q9F663
- Ligands
- ZXM, SO4
- Pockets
- 3 · best druggability 0.71
Structure
x-ray diffraction · 1 distinct chain · 42% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Carbapenem-hydrolyzing beta-lactamase kpc (EC 3.5.2.6) | protein | 265 | 42% helix, 17% strand | Q9F663 |
Ligands and binding sites
- ZXM · 1-{(2R)-2-(dihydroxyboranyl)-2-[(thiophen-2-ylacetyl) amino]ethyl}-1H-1,2,3-triazole-4-carboxylic acid · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 6 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 843 | 0.71 | 0.76 | 72 | empty |
| 2 | 119 | 0.36 | 0.74 | 19 | ZXM, SO4 |
| 3 | 63 | 0.36 | 0.78 | 16 | ZXM |
Interfaces
1 interface between chains.
- A–B · 261 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent, 2 disulfide (covalent ligand, disulfide).
Compared structures
- 5EEC · Crystal structure of KPC-2 beta-lactamase in complex with the S02030 boronic acid… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9F663 · AlphaFold monomer V2.0 prediction for carbapenem-hydrolyzing beta- lactamase kpc (Q9F663) · 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 Q9F663
- Elsewhere: RCSB PDB 5EEC · PDBe 5EEC · UniProt Q9F663
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