Structure of PDB 2ybf Chain A Binding Site BS01

Receptor Information
>2ybf Chain A (length=150) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
TPARRRLMRDFKRLQEDPPVGVSGAPSENNIMQWNAVIFGPEGTPFEDGT
FKLVIEFSEEYPNKPPTVRFLSKMFHPNVYADGSICLDILQNRWSPTYDV
SSILTSIQSLLDEPNPNSPANSQAAQLYQENKREYEKRVSAIVEQSWNDS
Ligand information
>2ybf Chain B (length=21) Species: 9606 (Homo sapiens) [Search peptide sequence] [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
KYRKKHKSEFQLLVDQARKGY
Receptor-Ligand Complex Structure
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PDB2ybf E3 Ligase Rad18 Promotes Monoubiquitination Rather Than Ubiquitin Chain Formation by E2 Enzyme Rad6.
Resolution2.0 Å
Binding residue
(original residue number in PDB)		S25 G26 S29 E30 N37 F41 G42 E49 D50 K54 L73 D151 S152
Binding residue
(residue number reindexed from 1)		S23 G24 S27 E28 N35 F39 G40 E47 D48 K52 L71 D149 S150
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.
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

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:2ybf, PDBe:2ybf, PDBj:2ybf
PDBsum2ybf
PubMed21422291
UniProtP63146|UBE2B_HUMAN Ubiquitin-conjugating enzyme E2 B (Gene Name=UBE2B)

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