MolNFT v1 · #139749 · protein

Crystal structure of lysk from thermus thermophilus in complex with lysine

5XOY · [lysw]-lysine hydrolase: “Crystal structure of lysk from thermus thermophilus in complex with lysine”. X-ray diffraction, 2 ligands (LYS, SO4), 3 pockets (best druggability 0.72). MolNFT v1 #139749 on GenesisL1: 3D structure…

PDB: 5XOY
Type: protein
Length: 690 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: [lysw]-lysine hydrolase
EC: 3.5.1.-
UniProt: Q8VUS5
Ligands: LYS, SO4
Pockets: 3 · best druggability 0.72

Structure

x-ray diffraction · 2 distinct chains · 35% helix, 29% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	[lysw]-lysine hydrolase (EC 3.5.1.-)	protein	341	36% helix, 28% strand	Q8VUS5
B	[lysw]-lysine hydrolase (EC 3.5.1.-)	protein	349	34% helix, 29% strand	Q8VUS5

Ligands and binding sites

LYS · Lysine · ligand · chains A, B
SO4 · Sulfate ion · ion · 3 copies · chains A, B

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

Pockets

3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	375	0.72	0.83	62	LYS
2	581	0.65	0.76	57	empty
3	84	0.44	0.80	20	empty

Interfaces

1 interface between chains.

A–B · 1292 Å² buried · 10 hydrogen bonds · protein-protein

Compared structures

5XOY · Crystal structure of LysK from Thermus thermophilus in complex with Lysine · the same entry in another collection · chain A against A, TM-score 1.00
Q8VUS5 · AlphaFold monomer V2.0 prediction for [lysw]-lysine hydrolase (Q8VUS5) · a predicted model of the same protein · chain B 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 Q8VUS5
Elsewhere: RCSB PDB 5XOY · PDBe 5XOY · UniProt Q8VUS5

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