Structure of PDB 5gmk Chain y

Receptor sequence

>5gmky (length=82) Species: 559292 (Saccharomyces cerevisiae S288C) [Search protein sequence]

NGIPVKLLNEAQGHIVSLELTTGATYRGKLVESEDSMNVQLRDVIATEPQ
GAVTHMDQIFVRGSQIKFIVVPDLLKNAPLFK

3D structure

PDB

5gmk Structure of a yeast catalytic step I spliceosome at 3.4 angstrom resolution

Chain

Resolution

3.4 Å

3D
structure

Enzymatic activity

Enzyme Commision number

Interaction with ligand

Site #	Ligand	Ligand chain	Binding residues on receptor (original residue number in PDB)	Binding residues on receptor (residue number reindexed from 1)	Binding affinity
BS01	rna	y	R30 N41 R65 S67	R27 N38 R62 S64

Gene Ontology

	Biological Process
GO:0000245	spliceosomal complex assembly
GO:0000387	spliceosomal snRNP assembly
GO:0000395	mRNA 5'-splice site recognition
GO:0000398	mRNA splicing, via spliceosome
GO:0006396	RNA processing
GO:0006397	mRNA processing
GO:0008380	RNA splicing
GO:0036261	7-methylguanosine cap hypermethylation
GO:1903241	U2-type prespliceosome assembly

	Cellular Component
GO:0000243	commitment complex
GO:0005634	nucleus
GO:0005681	spliceosomal complex
GO:0005682	U5 snRNP
GO:0005685	U1 snRNP
GO:0005686	U2 snRNP
GO:0005687	U4 snRNP
GO:0005737	cytoplasm
GO:0005829	cytosol
GO:0034715	pICln-Sm protein complex
GO:0034719	SMN-Sm protein complex
GO:0046540	U4/U6 x U5 tri-snRNP complex
GO:0071001	U4/U6 snRNP
GO:0071004	U2-type prespliceosome
GO:0071011	precatalytic spliceosome
GO:0071013	catalytic step 2 spliceosome
GO:0097525	spliceosomal snRNP complex
GO:0097526	spliceosomal tri-snRNP complex
GO:1990904	ribonucleoprotein complex

External links

PDB	RCSB:5gmk, PDBe:5gmk, PDBj:5gmk
PDBsum	5gmk
PubMed	27445308
UniProt	P43321\|SMD3_YEAST Small nuclear ribonucleoprotein Sm D3 (Gene Name=SMD3)