Research workbench
Crystal structure of kpc-2 carbapenemase in complex with a phenyl boronic inhibitor.
Analyse Crystal structure of kpc-2 carbapenemase in complex with a phenyl boronic… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5LL7
- Type
- protein
- Length
- 264 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-lactamase
- EC
- 3.5.2.6
- UniProt
- A0A0H4IUK8
- Ligands
- 6YV
- Pockets
- 1 · best druggability 0.28
Structure
x-ray diffraction · 1 distinct chain · 43% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-lactamase (EC 3.5.2.6) | protein | 264 | 43% helix, 17% strand | A0A0H4IUK8 |
Ligands and binding sites
- 6YV · (~{E})-3-[2-(dihydroxyboranyl)phenyl]prop-2-enoic acid · ligand · chains A
- EDO · 1,2-ethanediol · additive · 3 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 71 | 0.28 | 0.73 | 18 | 6YV |
Modifications
Observed in the structure: 1 covalent, 1 disulfide (covalent ligand, disulfide).
Compared structures
- 5LL7 · Crystal structure of KPC-2 carbapenemase in complex with a phenyl boronic inhibitor. · the same entry in another collection · 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 A0A0H4IUK8
- Elsewhere: RCSB PDB 5LL7 · PDBe 5LL7 · UniProt A0A0H4IUK8
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