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Crystal structure of D179Y kpc-2 beta-lactamase

Analyse Crystal structure of D179Y kpc-2 beta-lactamase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7TBX
Type: protein
Length: 459 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
Pockets: 1 · best druggability 0.46

Structure

x-ray diffraction · 2 distinct chains · 42% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Carbapenem-hydrolyzing beta-lactamase kpc (EC 3.5.2.6)	protein	240	40% helix, 19% strand	Q9F663
B	Carbapenem-hydrolyzing beta-lactamase kpc (EC 3.5.2.6)	protein	219	44% helix, 19% strand	Q9F663

Pockets

1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	231	0.46	0.73	36	empty

Interfaces

1 interface between chains.

A–B · 159 Å² buried · 4 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 disulfide (disulfide).

Compared structures

7TBX · Crystal structure of D179Y KPC-2 beta-lactamase · 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 0.97

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 7TBX · PDBe 7TBX · UniProt Q9F663

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