MolNFT v1 · #126302 · protein

Structure of the tpr domain of SGT2 in complex with yeast SSA1 peptide fragment

5LYN · Small glutamine-rich tetratricopeptide repeat-containing…: “Structure of the tpr domain of SGT2 in complex with yeast SSA1 peptide fragment”. X-ray diffraction, 1 ligand (ZN), 1 pocket (best druggability 0.52). MolNFT v1 #126302 on…

PDB: 5LYN
Type: protein
Length: 280 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Small glutamine-rich tetratricopeptide repeat-containing protein 2…
UniProt: Q12118
Ligands: ZN
Pockets: 1 · best druggability 0.52

Structure

x-ray diffraction · 2 distinct chains · 79% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Small glutamine-rich tetratricopeptide repeat-containing protein 2	protein	133	83% helix, 0% strand	Q12118
C, D	Pro-thr-val-glu-glu-val-asp	protein	7	0% helix, 0% strand	—

Ligands and binding sites

ZN · Zinc ion · metal · 9 copies · chains A, B, D

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	223	0.52	0.76	31	empty

Interfaces

5 interfaces between chains.

A–D · 540 Å² buried · 10 hydrogen bonds · protein-protein
B–C · 498 Å² buried · 11 hydrogen bonds · protein-protein
A–B · 420 Å² buried · 9 hydrogen bonds · protein-protein
A–C · 41 Å² buried · 0 hydrogen bonds · protein-protein
B–D · 17 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

5LYN · Structure of the Tpr Domain of Sgt2 in complex with yeast Ssa1 peptide fragment · the same entry in another collection · chain A against A, TM-score 1.00
Q12118 · AlphaFold monomer V2.0 prediction for small glutamine-rich tetratricopeptide… · 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 Q12118
Elsewhere: RCSB PDB 5LYN · PDBe 5LYN · UniProt Q12118

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