Structure of PDB 8kdb Chain A

Receptor sequence
>8kdbA (length=2117) Species: 11216 (Human respirovirus 3) [Search protein sequence]
GTVSDILYPECHLNSPIVKGKIAQLHTIMSLPQPYDMDDDSILVITRQKI
KLNKLDKRQRSIRRLKLILTEKVNDLGKYTFIRYPEMSKEMFKLYIPGIN
SKVTELLLKADRTYSQMTDGLRDLWINVLSKLASKNDGSNYDLNEEINNI
SKVHTTYKSDKWYNPFKTWFTIKYDMRRLQKARNEITFNVGKDYNLLEDQ
KNFLLIHPELVLILDKQNYNGYLITPELVLMYCDVVEGRWNISACAKLDP
KLQSMYQKGNNLWEVIDKLFPIMGEKTFDVISLLEPLALSLIQTHDPVKQ
LRGAFLNHVLSEMELIFESGESIREFLSVDYIDKILDIFNESTIDEIAEI
FSFFRTFGHPPLEASIAAEKVRKYMYIEKQLKFDTVNKCHAIFCTIIING
YRERHGGQWPPVTLPDHAHEFIINAYGSNSAISYENAVDYYQSFIGIKFN
KFIEPQLDEDLTIYMKDKALSPKKSNWDTVYPASNLLYRTNASNESRRLV
EVFIADSKFDPHQILDYVESGDWLDDPEFNISYSLKEKEIKQEGRLFAKM
TYKMRATQVLSETLLANNIGKFFQENGMVKGEIELLKRLTTISISGVPRY
NEVSKKFEFKSTDIYNDGYETVSCFLTTDLKKYCLNWRYESTALFGETCN
QIFGLNKLFNWLHPRLEGSTIYVGDPYCPPSDKEHISLEDHPDSGFYVHN
PRGGIEGFCQKLWTLISISAIHLAAVRIGVRVTAMVQGDNQAIAVTTRVP
NNYDYRIKKEIVYKDVVRFFDSLREVMDDLGHELKLNETIISSKMFIYSK
RIYYDGRILPQALKALSRCVFWSETVIDETRSASSNLATSFAKAIENGYS
PVLGYACSIFKNIQQLYIALGMNINPTITQNIKDQYFKNSNWMQYASLIP
ASVGGFNYMAMSRCFVRNIGDPSVAALADIKRFIKANLLDRSVLYRIMNQ
EPGESSFLDWASDPYSCNLPQSQNITTMIKNITARNVLQDSPNPLLSGLF
TNTMIEEDEELAEFLMDRKVILPRVAHDILDNSLTGIRNAIAGMLDTTKS
LIRVGINRGGLTYSLLRKISNYDLVQYETLSRTLRLIVSDKIRYEDMCSV
DLAIALRQKMWIHLSGGRMISGLETPDPLELLSGVVITGSEHCKICYSSD
GTNPYTWMYLPGNIKIGSAETGVSSLRVPYFGSVTDERSEAQLGYIKNLS
KPAKAAIRIAMIYTWAFGNDEISWMEASQIAQTRANFTLDSLKILTPVAT
STNLSHRKFSSTSLIRVSRFITMSNDNMSIKEANETKDTNLIYQQIMLTG
LSVFEYLFRLKETTGHNPIVMHLHIEDECCIKESFNDEHINPESTLELIR
YPESNEFIYDKDPLKDVDLSKLMVIKDHSYTIDMNYWDDTDIIHAISICT
AITIADTMSQLDRDNLKEIIVIANDDDINSLITEFLTLDILVFLKTFGGL
LVNQFAYTLYSLKIEGRDLIWDYIMRTLRDTSHSILKVLSNALSHPKVFK
RFWDCGVLNPIYGPNTASQDQIKLALSICEYALDLFMREWLNGVSLEIYI
CDSDMEVANDRKQAFISRHLSFVCCLAEIASFGPNLLNLTYLERLDLLKQ
YLELNIKEDPTLKYVQISGLLIKSFPSTVTYVRKTAIKYLRIRGISPPEV
NIVKTINDNCNKDNKGNKINNFWGLALKNYQVLKIRSILPQGGNYLSHQL
RLFGINSTSCLKALELSQILMKEVNKDKDRLFLGEGAGAMLACYDATLGP
AINYYNSGLNITDVIGQRELKIFPSEVSLVGKKLGNVTQILNRVKVLFNG
NPNSTWIGNMECESLIWSELNDKSIGLVHCDMEGAIGKSEETVLHEHYSV
IRITYLIGDDDVVLVSKIIPTITPNWSRILYLYKLYWKDVSIISLKTSNP
ASTELYLISKDAYCTIMEPSEVVLSKLKRLSLLEENNLLKWIILSKKRNN
EWLHHEIKEGERDYGVMRPYHMALQIFGFQINLNHLAKEFLSTPDLTNIN
NIIQSFQRTIKDVLFEWININKGKLRLLSRRLVLSWISLSLSTRLLTGRF
PDEKFEHRAQTGYVSLADTDLESLKLLSKNIIKNYRECIGSISYWFLTKE
VKILMKLIGGAKLLGIP
3D structure
PDB8kdb Structural basis for dimerization of a paramyxovirus polymerase complex.
ChainA
Resolution2.7 Å
3D
structure
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Enzymatic activity
Enzyme Commision number 2.1.1.-
2.1.1.375: NNS virus cap methyltransferase.
2.7.7.48: RNA-directed RNA polymerase.
2.7.7.88: GDP polyribonucleotidyltransferase.
3.6.1.-
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 MG A Y667 D773 Y633 D739
BS02 ZN A C1177 H1364 H1366 C1143 H1322 H1324
BS03 ZN A C1132 E1164 C1371 C1098 E1130 C1329
Gene Ontology
Molecular Function
GO:0003924 GTPase activity
GO:0003968 RNA-dependent RNA polymerase activity
GO:0004482 mRNA 5'-cap (guanine-N7-)-methyltransferase activity
GO:0005524 ATP binding
GO:0008168 methyltransferase activity
GO:0016740 transferase activity
GO:0016787 hydrolase activity
GO:0034062 5'-3' RNA polymerase activity
Biological Process
GO:0001172 RNA-templated transcription
GO:0006139 nucleobase-containing compound metabolic process
GO:0006370 7-methylguanosine mRNA capping
GO:0032259 methylation
GO:0106005 RNA 5'-cap (guanine-N7)-methylation
Cellular Component
GO:0005737 cytoplasm
GO:0030430 host cell cytoplasm
GO:0044423 virion component

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:8kdb, PDBe:8kdb, PDBj:8kdb
PDBsum8kdb
PubMed38605025
UniProtO89238

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