Research workbench
Kpc-2 N170A mutant bound to hydrolyzed ampicillin at 1.65 a
Analyse Kpc-2 N170A mutant bound to hydrolyzed ampicillin at 1.65 a in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6XD7
- Type
- protein
- Length
- 266 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
- ZZ7
- Pockets
- 1 · best druggability 0.32
Structure
x-ray diffraction · 1 distinct chain · 47% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Carbapenem-hydrolyzing beta-lactamase kpc (EC 3.5.2.6) | protein | 266 | 47% helix, 17% strand | Q9F663 |
Ligands and binding sites
- ZZ7 · (2R,4S)-2-[(R)-{[(2R)-2-amino-2-phenylacetyl]amino}(carboxy)methyl]-5,5-dimethyl-1,3-thiazolidine-4-carboxylic acid · ligand · 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 | 83 | 0.32 | 0.74 | 20 | ZZ7 |
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 6XD7 · KPC-2 N170A mutant bound to hydrolyzed ampicillin at 1.65 A · 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 6XD7 · PDBe 6XD7 · UniProt Q9F663
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