Structure of PDB 5egs Chain D

Receptor sequence
>5egsD (length=334) Species: 9606 (Homo sapiens) [Search protein sequence]
RTKRERDQLYYECYSDVSVHEEMIADRVRTDAYRLGILRNWAALRGKTVL
DVGAGTGILSIFCAQAGARRVYAVEASAIWQQAREVVRFNGLEDRVHVLP
GPVETVELPEQVDAIVSEWMGYGLLHESMLSSVLHARTKWLKEGGLLLPA
SAELFIVPISDQMLEWRLGFWSQVKQHYGVDMSCLEGFATRCLMGHSEIV
VQGLSGEDVLARPQRFAQLELSRAGLEQELEAGVGGRFRCSCYGSAPMHG
FAIWFQVTFPGGPLVLSTSPFHPATHWKQALLYLNEPVQVEQDTDVSGEI
TLLPSRDNPRRLRVLLRYKVGDQEEKTKDFAMED
3D structure
PDB5egs Discovery of a Potent Class I Protein Arginine Methyltransferase Fragment Inhibitor.
ChainD
Resolution2.15 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) D26 E118 E127 H276
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 D Y47 Y48 Y51 M60 R66 G90 A91 G92 I95 E112 A113 M166 S169 Y10 Y11 Y14 M23 R29 G53 A54 G55 I58 E75 A76 M129 S132
BS02 5NR D Y51 V56 M60 E155 M157 Y159 E164 H317 Y14 V19 M23 E118 M120 Y122 E127 H276 MOAD: Kd=0.97uM
BindingDB: Kd=970nM,IC50=21000nM
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:5egs, PDBe:5egs, PDBj:5egs
PDBsum5egs
PubMed26824386
UniProtQ96LA8|ANM6_HUMAN Protein arginine N-methyltransferase 6 (Gene Name=PRMT6)

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