Research workbench

Kpc-2 F72Y mutant with acylated imipenem

Analyse Kpc-2 F72Y mutant with acylated imipenem in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7LLH
Type: protein
Length: 520 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
Ligands: IM2
Pockets: 4 · best druggability 0.39

Structure

x-ray diffraction · 1 distinct chain · 43% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Carbapenem-hydrolyzing beta-lactamase kpc (EC 3.5.2.6)	protein	260	43% helix, 17% strand	Q9F663

Ligands and binding sites

IM2 · (5R)-5-[(1S,2R)-1-formyl-2-hydroxypropyl]-3-[(2-{[(E)-iminomethyl]amino}ethyl)sulfanyl]-4,5-dihydro-1H-pyrrole-2-carbox ylic acid · ligand · 2 copies · chains A, B

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	118	0.39	0.74	20	empty
2	98	0.38	0.76	18	IM2
3	64	0.37	0.78	18	empty
4	105	0.37	0.75	19	IM2

Interfaces

1 interface between chains.

A–B · 394 Å² buried · 3 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 covalent, 2 disulfide (covalent ligand, disulfide).

Compared structures

7LLH · KPC-2 F72Y mutant with acylated imipenem · 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 7LLH · PDBe 7LLH · UniProt Q9F663

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