Structure of PDB 6yov Chain H Binding Site BS02

Receptor Information
>6yov Chain H (length=92) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
RKESYSIYVYKVLKQVHPDTGISSKAMGIMNSFVNDIFERIAGEASRLAH
YNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTSA
Ligand information
Ligand IDPTD
InChIInChI=1S/C5H8O2/c6-4-2-1-3-5-7/h4-5H,1-3H2
InChIKeySXRSQZLOMIGNAQ-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0C(CC=O)CC=O
ACDLabs 10.04
CACTVS 3.341		O=CCCCC=O
FormulaC5 H8 O2
NamePENTANEDIAL
ChEMBLCHEMBL1235482
DrugBankDB03266
ZINCZINC000001729593
PDB chain6yov Chain H Residue 201 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB6yov Mechanisms of OCT4-SOX2 motif readout on nucleosomes.
Resolution3.42 Å
Binding residue
(original residue number in PDB)		K44 K47
Binding residue
(residue number reindexed from 1)		K11 K14
Annotation score1
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0001530 lipopolysaccharide binding
GO:0003677 DNA binding
GO:0005515 protein binding
GO:0030527 structural constituent of chromatin
GO:0046982 protein heterodimerization activity
Biological Process
GO:0002227 innate immune response in mucosa
GO:0006325 chromatin organization
GO:0006334 nucleosome assembly
GO:0010804 negative regulation of tumor necrosis factor-mediated signaling pathway
GO:0019731 antibacterial humoral response
GO:0031640 killing of cells of another organism
GO:0042742 defense response to bacterium
GO:0050829 defense response to Gram-negative bacterium
GO:0050830 defense response to Gram-positive bacterium
GO:0061644 protein localization to CENP-A containing chromatin
GO:0061844 antimicrobial humoral immune response mediated by antimicrobial peptide
Cellular Component
GO:0000786 nucleosome
GO:0005615 extracellular space
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005694 chromosome
GO:0005829 cytosol
GO:0005886 plasma membrane
GO:0043505 CENP-A containing nucleosome

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:6yov, PDBe:6yov, PDBj:6yov
PDBsum6yov
PubMed32327602
UniProtP06899|H2B1J_HUMAN Histone H2B type 1-J (Gene Name=H2BC11)

[Back to BioLiP]