MolNFT v1 · #145891 · protein
Crystal structure of kpc-2 complexed with compound 9
6D19 · Carbapenem-hydrolyzing beta-lactamase kpc: “Crystal structure of kpc-2 complexed with compound 9”. X-ray diffraction, 1 ligand (YKG), 1 pocket (best druggability 0.34). MolNFT v1 #145891 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6D19
- Type
- protein
- Length
- 269 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
- Q9F663
- Ligands
- YKG
- Pockets
- 1 · best druggability 0.34
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 | 269 | 43% helix, 17% strand | Q9F663 |
Ligands and binding sites
- YKG · [(5-bromo-7-methyl-2-oxo-2H-1-benzopyran-4-yl) methyl]phosphonic acid · ligand · 3 copies · chains A
- GOL · Glycerol · additive · 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 | 0.34 | 0.77 | 14 | YKG |
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 6D19 · Crystal structure of KPC-2 complexed with compound 9 · 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 0.99
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 6D19 · PDBe 6D19 · UniProt Q9F663
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