MolNFT v1 · #55544 · protein

Yeast betaprime cop 1-304 with ktktn motif

2YNN · Coatomer subunit beta': “Yeast betaprime cop 1-304 with ktktn motif”. X-ray diffraction, 1 ligand (SO4), 2 pockets (best druggability 0.80). MolNFT v1 #55544 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 2YNN
Type: protein
Length: 308 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Coatomer subunit beta'; Ktktn motif
UniProt: P41811
Ligands: SO4
Pockets: 2 · best druggability 0.80

Structure

x-ray diffraction · 2 distinct chains · 3% helix, 54% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Coatomer subunit beta'	protein	300	3% helix, 55% strand	P41811
P	Ktktn motif	protein	8	0% helix, 0% strand	—

Ligands and binding sites

SO4 · Sulfate ion · ion · 3 copies · chains A

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	668	0.80	0.85	54	SO4
2	61	0.27	0.73	15	empty

Interfaces

1 interface between chains.

A–P · 355 Å² buried · 12 hydrogen bonds · protein-protein

Compared structures

2YNN · yeast betaprime COP 1-304 with KTKTN motif · the same entry in another collection · chain A against A, TM-score 1.00
P41811 · AlphaFold monomer V2.0 prediction for coatomer subunit beta' (P41811) · 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 P41811
Elsewhere: RCSB PDB 2YNN · PDBe 2YNN · UniProt P41811

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