Structure of PDB 2ybf Chain A

Receptor sequence

>2ybfA (length=150) Species: 9606 (Homo sapiens) [Search protein sequence]

TPARRRLMRDFKRLQEDPPVGVSGAPSENNIMQWNAVIFGPEGTPFEDGT
FKLVIEFSEEYPNKPPTVRFLSKMFHPNVYADGSICLDILQNRWSPTYDV
SSILTSIQSLLDEPNPNSPANSQAAQLYQENKREYEKRVSAIVEQSWNDS

3D structure

PDB

2ybf E3 Ligase Rad18 Promotes Monoubiquitination Rather Than Ubiquitin Chain Formation by E2 Enzyme Rad6.

Chain

Resolution

2.0 Å

3D
structure

Catalytic site residues are labeled in the structure
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Enzymatic activity

Catalytic site (original residue number in PDB)	C88
Catalytic site (residue number reindexed from 1)	C86
Enzyme Commision number	2.3.2.23: E2 ubiquitin-conjugating enzyme.

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	peptide	A	S25 G26 S29 E30 N37 F41 G42 E49 D50 K54 L73 D151 S152	S23 G24 S27 E28 N35 F39 G40 E47 D48 K52 L71 D149 S150

Gene Ontology

	Molecular Function
GO:0004842	ubiquitin-protein transferase activity
GO:0005515	protein binding
GO:0005524	ATP binding
GO:0016740	transferase activity
GO:0019787	ubiquitin-like protein transferase activity
GO:0031625	ubiquitin protein ligase binding
GO:0061631	ubiquitin conjugating enzyme activity

	Biological Process
GO:0000209	protein polyubiquitination
GO:0001701	in utero embryonic development
GO:0006281	DNA repair
GO:0006301	postreplication repair
GO:0006325	chromatin organization
GO:0006511	ubiquitin-dependent protein catabolic process
GO:0006915	apoptotic process
GO:0006974	DNA damage response
GO:0007283	spermatogenesis
GO:0007288	sperm axoneme assembly
GO:0009410	response to xenobiotic stimulus
GO:0009411	response to UV
GO:0010845	positive regulation of reciprocal meiotic recombination
GO:0016567	protein ubiquitination
GO:0032446	protein modification by small protein conjugation
GO:0035234	ectopic germ cell programmed cell death
GO:0043066	negative regulation of apoptotic process
GO:0043161	proteasome-mediated ubiquitin-dependent protein catabolic process
GO:0045141	meiotic telomere clustering
GO:0050821	protein stabilization
GO:0051026	chiasma assembly
GO:0051093	negative regulation of developmental process
GO:0051865	protein autoubiquitination
GO:0070193	synaptonemal complex organization
GO:0070534	protein K63-linked ubiquitination
GO:0070936	protein K48-linked ubiquitination
GO:0070979	protein K11-linked ubiquitination
GO:0090263	positive regulation of canonical Wnt signaling pathway
GO:1901874	negative regulation of post-translational protein modification
GO:2000242	negative regulation of reproductive process

	Cellular Component
GO:0000785	chromatin
GO:0001741	XY body
GO:0005634	nucleus
GO:0005654	nucleoplasm
GO:0005657	replication fork
GO:0005737	cytoplasm
GO:0005886	plasma membrane
GO:0033503	HULC complex

View graph for
Molecular Function

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Biological Process

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Cellular Component

External links

PDB	RCSB:2ybf, PDBe:2ybf, PDBj:2ybf
PDBsum	2ybf
PubMed	21422291
UniProt	P63146\|UBE2B_HUMAN Ubiquitin-conjugating enzyme E2 B (Gene Name=UBE2B)

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