Structure of PDB 5e8r Chain A

Receptor sequence
>5e8rA (length=332) Species: 9606 (Homo sapiens) [Search protein sequence]
ERDQLYYECYSDVSVHEEMIADRVRTDAYRLGILRNWAALRGKTVLDVGA
GTGILSIFCAQAGARRVYAVEASAIWQQAREVVRFNGLEDRVHVLPGPVE
TVELPEQVDAIVSEWMGYGLLHESMLSSVLHARTKWLKEGGLLLPASAEL
FIVPISDQMLEWRLGFWSQVKQHYGVDMSCLEGFATRCLMGHSEIVVQGL
SGEDVLARPQRFAQLELSRAGLEQELEAGVGGRFRCSCYGSAPMHGFAIW
FQVTFPGGEKPLVLSTSPFHPATHWKQALLYLNEPVQVEQDTDVSGEITL
LPSRDNPRRLRVLLRYKVGDQEEKTKDFAMED
3D structure
PDB5e8r A Potent, Selective, and Cell-Active Inhibitor of Human Type I Protein Arginine Methyltransferases.
ChainA
Resolution2.55 Å
3D
structure
Catalytic site residues are labeled in the structure
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Enzymatic activity
Catalytic site (original residue number in PDB) D63 E155 E164 H317
Catalytic site (residue number reindexed from 1) D22 E114 E123 H274
Enzyme Commision number 2.1.1.319: type I protein arginine methyltransferase.
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 SAH A Y51 M60 R66 G90 E112 A113 P139 V140 E141 M166 S169 Y10 M19 R25 G49 E71 A72 P98 V99 E100 M125 S128
BS02 5L6 A Y51 V56 E59 M60 E155 M157 Y159 H163 E164 H317 Y10 V15 E18 M19 E114 M116 Y118 H122 E123 H274 PDBbind-CN: -logKd/Ki=8.70,Kd=2nM
BindingDB: IC50=4.0nM,Ki=0.8nM,Kd=6nM
Gene Ontology
Molecular Function
GO:0003682 chromatin binding
GO:0005515 protein binding
GO:0008168 methyltransferase activity
GO:0008469 histone arginine N-methyltransferase activity
GO:0016274 protein-arginine N-methyltransferase activity
GO:0035241 protein-arginine omega-N monomethyltransferase activity
GO:0035242 protein-arginine omega-N asymmetric methyltransferase activity
GO:0042054 histone methyltransferase activity
GO:0042393 histone binding
GO:0044020 histone H4R3 methyltransferase activity
GO:0070611 histone H3R2 methyltransferase activity
GO:0070612 histone H2AR3 methyltransferase activity
GO:0140938 histone H3 methyltransferase activity
Biological Process
GO:0000122 negative regulation of transcription by RNA polymerase II
GO:0006281 DNA repair
GO:0006284 base-excision repair
GO:0006325 chromatin organization
GO:0006338 chromatin remodeling
GO:0010821 regulation of mitochondrion organization
GO:0018216 peptidyl-arginine methylation
GO:0032259 methylation
GO:0036211 protein modification process
GO:0045652 regulation of megakaryocyte differentiation
GO:0045892 negative regulation of DNA-templated transcription
GO:0090398 cellular senescence
GO:1901796 regulation of signal transduction by p53 class mediator
GO:2000059 negative regulation of ubiquitin-dependent protein catabolic process
Cellular Component
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005730 nucleolus

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:5e8r, PDBe:5e8r, PDBj:5e8r
PDBsum5e8r
PubMed26598975
UniProtQ96LA8|ANM6_HUMAN Protein arginine N-methyltransferase 6 (Gene Name=PRMT6)

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