Structure of PDB 6syt Chain A

Receptor sequence

>6sytA (length=1896) Species: 9606 (Homo sapiens)

AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
AAAAAAAAAAAAAAAAAAAAAFSTNFRDTVDILVGSLTQQVSGWLQSLEA
FSTTLLGQFLEDMEAYAEDLSSVSLPKLAALLRVFSTVVRSIAYVTDVLY
RVMRCVTAANQVFFSEAVLTAANECVGVLLGSLDPSMTIHCDMVITYGLD
QLENCQTCGTDYIISVLNLLTLIVEQINTKLPSSFVEKLFIPSSKLLFLR
YHKEKEVVAVAHAVYQAVLSLKNIPVLETAYKLILGEMTCALNNLLHSLQ
LPEACSEIKHEAFKNHVFNVDNAKFVVIFDLSALTTIGNAKNLSPTVFAL
LSKNLMIVHSDLAVHFPAIQYAVLYTLYSHCTRHDHFISSSKKHFSIILN
LLGILLKKDNLNQDTRKLLMTWALEAAVLMRKSETYAPLFSLPSFHKFCK
GLLANTLVEDVNICLQACSSLHALSSSLPDDLLQRCVDVCRVQLVHSGTR
IRQAFGKLLKSIPLDVVLSNNNHTEIQEISLALRSHMSKAPSNTFHPQDF
SDVISFILYGNSHRTNWLERLFYSCQRLDKTIPRNLLKTDAVLWQWAIWE
AAQFTVLSKLRTPLGRAQDTFQTIEGIIRSLAAHTLNPDQDVSQWTTADN
DEGHGNNQLRLVLLLQYLENLEKLMYNAYEGCANALTRTFFYTNRQTCQD
WLTRIRLSIMRVGLLAGQPAVTVRHGFDLLTEMKTNELEVTIMMVVEALC
ELHCPEAIQGIAVWSSSINLLWINSVAQQAEGRFEKASVEYQEHLCAMTG
VDCCISSFDKSVLTLANSSPEVINYLGNKACECYISIADWAAVQEWQNAI
HDLKKSTSSTSLNLKADFNYIKSLSSFESGKFVECTEQLELLPGENINLD
MKKLLPNMLSPDPRELQKSIEVQLLRSSVCLATALNWQSITENVVKYLKQ
TSRIAIGPLRLSTLTVSQSLPVLSTLQLYCSSALENTVSNRLSTEDCLIP
LFSEALRSCKQHDVRPWMQALRYTMYQNQLLEKIKEQTVPIRSHLMELGL
TAAKFARKRGNVSLATRLLAQCSETTAQDLVQHFKKWGPELDIEKTKLLY
TAGQSTHAMEMLSSCAISFCKSVKAEYAVAKSILTLAKWIQAEWKEISGQ
LKQVYRAQHQLSTLSKNILTLIELPSESESTVHIGVGEPDFILGQLYHLS
SVQAPEVAKSWAALASWAYRWGRKVVDNASAAAAAAAAAAAAAAAAAAAA
AAAAAAAAAAAAAAAAAAAAAAEGVIKVWRKVVDRIFSLYKLSCSAYFTF
LKLNASTDDMIVMATLRLLRLLVKHAGELRQYLEHGLETPWRGIIPQLFS
RLNHPEVYVRQSICNLLCRVAQDSPHLILYPAIVGTIQAMMQDCYSKIVD
KLSSANPTMVLQVQMLVAELRRVTWDELWLGVLLQQHMYVLAAAAAAAAA
AAAAAAAPHEKWFQDNYGDAIENALEKLKAAAAAAAAAAAAAAAAYILRL
EEITNTEIALPGVTIHSVGTITILPTKPKKLLFLGSDSYPYLFKGLEDLH
LDERIMQFLSIVNTMFATINRQETPRFHARHYSVTPLGTRSGLIQWVDGA
TPLFGLYKRWQQREAALQAQKAAAAAAAAAAAAAAAAAAWPLHVMKAVLE
ELMEATPPNLLAKELWSSCTTPDEWWRVTQSYARSTAVMSMVGYIIGLGA
RHLDNVLIDMTTGEVVHIDYNVCFEKGKSLRVPEKVPFRMTQNIETALGV
TGVEGVFRLSCEQVLHIMRRGRETLLTLLEAFVYDPLVDWTSYAVSVWKR
VKAKLEGRDVDPNRRMSVAEQVDYVIKEATNLDNLAQLYEGWTAWV

3D structure

• PDB: 6syt InsP6binding to PIKK kinases revealed by the cryo-EM structure of an SMG1-SMG8-SMG9 complex.
• Chain: A
• Resolution: 3.45 Å

Enzymatic activity

• Enzyme Commision number: 2.7.11.1: non-specific serine/threonine protein kinase.

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	IHP	A	K1386 K1434 K1523 K1530 K1617	K1060 K1108 K1181 K1188 K1259

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0004672 protein kinase activity
• GO:0004674 protein serine/threonine kinase activity
• GO:0004697 diacylglycerol-dependent serine/threonine kinase activity
• GO:0005515 protein binding
• GO:0005524 ATP binding
• GO:0042162 telomeric DNA binding
• GO:0044024 histone H2AS1 kinase activity
• GO:0046872 metal ion binding
• GO:0106310 protein serine kinase activity

Biological Process

• GO:0000184 nuclear-transcribed mRNA catabolic process, nonsense-mediated decay
• GO:0006281 DNA repair
• GO:0006338 chromatin remodeling
• GO:0006406 mRNA export from nucleus
• GO:0006974 DNA damage response
• GO:0016310 phosphorylation
• GO:0018105 peptidyl-serine phosphorylation
• GO:0019219 regulation of nucleobase-containing compound metabolic process
• GO:0032204 regulation of telomere maintenance
• GO:0046777 protein autophosphorylation
• GO:0046854 phosphatidylinositol phosphate biosynthetic process

Cellular Component

• GO:0005634 nucleus
• GO:0005654 nucleoplasm
• GO:0005737 cytoplasm
• GO:0005829 cytosol
• GO:0033391 chromatoid body

External links

• PDB: RCSB:6syt, PDBe:6syt, PDBj:6syt
• PDBsum: 6syt
• PubMed: 31792449
• UniProt: Q96Q15|SMG1_HUMAN Serine/threonine-protein kinase SMG1 (Gene Name=SMG1)