MolNFT v1 · #169477 · protein

Apo kpc-2 N170A mutant at 1.20 a

6XD5 · Carbapenem-hydrolyzing beta-lactamase kpc: “Apo kpc-2 N170A mutant at 1.20 a”. X-ray diffraction, 1 ligand (SO4), 1 pocket (best druggability 0.28). MolNFT v1 #169477 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6XD5
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: SO4
Pockets: 1 · best druggability 0.28

Structure

x-ray diffraction · 1 distinct chain · 41% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Carbapenem-hydrolyzing beta-lactamase kpc (EC 3.5.2.6)	protein	269	41% helix, 17% strand	Q9F663

Ligands and binding sites

SO4 · Sulfate ion · ion · 4 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.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	58	0.28	0.74	17	SO4

Modifications

Observed in the structure: 1 disulfide (disulfide).

Compared structures

6XD5 · Apo KPC-2 N170A mutant at 1.20 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 1.00

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 6XD5 · PDBe 6XD5 · UniProt Q9F663

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