MolNFT v1 · #126892 · protein
Crystal structure of kpc-2 carbapenemase in complex with a phenyl boronic inhibitor.
5MGI · Carbapenem-hydrolyzing beta-lactamase kpc: “Crystal structure of kpc-2 carbapenemase in complex with a phenyl boronic inhibitor.”. X-ray diffraction, 1 ligand (6YV), 1 pocket (best druggability 0.33). MolNFT v1 #126892 on GenesisL1…
- PDB
- 5MGI
- Type
- protein
- Length
- 264 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Carbapenem-hydrolyzing beta-lactamase kpc
- EC
- 3.5.2.6
- UniProt
- Q848S6
- Ligands
- 6YV
- Pockets
- 1 · best druggability 0.33
Structure
x-ray diffraction · 1 distinct chain · 43% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Carbapenem-hydrolyzing beta-lactamase kpc (EC 3.5.2.6) | protein | 264 | 43% helix, 17% strand | Q848S6 |
Ligands and binding sites
- 6YV · (~{E})-3-[2-(dihydroxyboranyl)phenyl]prop-2-enoic acid · ligand · 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 | 92 | 0.33 | 0.74 | 18 | 6YV |
Modifications
Observed in the structure: 1 covalent, 1 disulfide (covalent ligand, disulfide).
Compared structures
- 5MGI · 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
- Q848S6 · AlphaFold monomer V2.0 prediction for carbapenem-hydrolyzing beta- lactamase kpc (Q848S6) · 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 Q848S6
- Elsewhere: RCSB PDB 5MGI · PDBe 5MGI · UniProt Q848S6
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