Structure of PDB 6z3r Chain A

Receptor sequence

>6z3rA (length=1943) Species: 9606 (Homo sapiens)

AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
AAAAAAAAAAAAAAAAAAAALETVGEKKAFSSVMQLVMTSLQSILENVDT
PELLCKCVKCILLVARCYPHIFSTNFRDTVDILVGSLTQQVSGWLQSLEA
FSTTLLGQFLEDMEAYAEDLSSVSLPKLAALLRVFSTVVRSIAYVTDVLY
RVMRCVTAANQVFFSEAVLTAANECVGVLLGSLDPSMTIHCDMVITYGLD
QLENCQTCGTDYIISVLNLLTLIVEQINTKLPSSFVEKLFIPSSKLLFLR
YHKEKEVVAVAHAVYQAVLSLKNIPVLETAYKLILGEMTCALNNLLHSLQ
LPEACSEIKHEAFKNHVFNVDNAKFVVIFDLSALTTIGNAKNWALSPTVF
ALLSKNLMIVHSDLAVHFPAIQYAVLYTLYSHCTRHDHFISSSTVTTATK
KHFSIILNLLGILLKKDNLNQDTRKLLMTWALEAAVLMRKSETYAPLFSL
PSFHKFCKGLLANTLVEDVNICLQACSSLHALSSSLPDDLLQRCVDVCRV
QLVHSGTRIRQAFGKLLKSIPLDVVLSNNKHTEIQEISLALRSHMSKAPS
NTFHPQDFSDVISFILYGNSHRTNWLERLFYSCQRLDKTIPRNLLKTDAV
LWQWAIWEAAQFTVLSKLRTPLGRAQDTFQTIEGIIRSLAAHTLNPDQDV
SQWTTADNDEGHGNNQLRLVLLLQYLENLEKLMYNAYEGCANALTSPPKV
IRTFFYTNRQTCQDWLTRIRLSIMRVGLLAGQPAVTVRHGFDLLTEMKTN
ELEVTIMMVVEALCELHCPEAIQGIAVWSSSINLLWINSVAQQAEGRFEK
ASVEYQEHLCAMTGVDCCISSFDKSVLTLANSSPEVINYLGNKACECYIS
IADWAAVQEWQNSIHDLKKSTSSTSLNLKADFNYIKSLSSFESGKFVECT
EQLELLPGENINLDMKKLLPNMLSPDPRELQKSIEVQLLRSSVCLATALN
WQSITENVVKYLKQTSRIAIGPLRLSTLTVSQSLPVLSTLQLYCSSALEN
TVSNRLSTEDCLIPLFSEALRSCKQHDVRPWMQALRYTMYQNQLLEKIKE
QTVPIRSHLMELGLTAAKFARKRGNVSLATRLLAQCSETTAQDLVQHFKK
WGPELDIEKTKLLYTAGQSTHAMEMLSSCAISFCKSVKAEYAVAKSILTL
AKWIQAEWKEISGQLKQVYRAQHQLSTLSKNILTLIELPSIESESTVHIG
VGEPDFILGQLYHLSSVQAPEVAKSWAALASWAYRWGRKVVDNASAAAAA
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAEGVIKVWRKVVDR
IFSLYKLSCSAYFTFLKLNAQSTDDMIVMATLRLLRLLVKHAGELRQYLE
HGLETTPTAPWRGIIPQLFSRLNHPEVYVRQSICNLLCRVAQDSPHLILY
PAIVGTIQAMMQDCYSKIVDKLSSANPTMVLQVQMLVAELRRVTWDELWL
GVLLQQHMYVLRRIQQLEDEVKRVQNNPHEKWFQDNYGDAIENALEKLKA
AAAAAAAAAAAAAAAYILRLEEIAAMTNTEIALPGEVSARDTVTIHSVGG
TITILPTKTKPKKLLFLGSDGKSYPYLFKGLEDLHLDERIMQFLSIVNTM
FATINRQETPRFHARHYSVTPLGTRSGLIQWVDGATPLFGLYKRWQQREA
ALQAQKIVPRPSELYYSKIGPALKTVGLSLDVSRRDWPLHVMKAVLEELM
EATPPNLLAKELWSSCTTPDEWWRVTQSYARSTAVMSMVGYIIGLGDRHL
DNVLIDMTTGEVVHIDYNVCFEKGKSLRVPEKVPFRMTQNIETALGVTGV
EGVFRLSCEQVLHIMRRGRETLLTLLEAFVYDPLVDWTSYAVSVWKRVKA
KLEGRDVDPNRRMSVAEQVDYVIKEATNLDNLAQLYEGWTAWV

3D structure

• PDB: 6z3r Structure of substrate-bound SMG1-8-9 kinase complex reveals molecular basis for phosphorylation specificity.
• Chain: A
• Resolution: 2.97 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	peptide	A	D2335 H2337 D2339 V2367 Y3654	D1797 H1799 D1801 V1829 Y1936
BS02	ANP	A	T2133 K2134 W2207 I2353	T1607 K1608 W1681 I1815
BS03	IHP	A	K1386 R1433 K1434 K1489 K1523 K1530 K1617	K1074 R1121 K1122 K1161 K1195 K1202 K1274

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:0016301 kinase activity
• 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:6z3r, PDBe:6z3r, PDBj:6z3r
• PDBsum: 6z3r
• PubMed: 32469312
• UniProt: Q96Q15|SMG1_HUMAN Serine/threonine-protein kinase SMG1 (Gene Name=SMG1)