Structure of PDB 8kdb Chain A Binding Site BS01

Receptor Information

>8kdb Chain A (length=2117) Species: 11216 (Human respirovirus 3)

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

Ligand information

• Ligand ID: MG
• InChI: InChI=1S/Mg/q+2
• InChIKey: JLVVSXFLKOJNIY-UHFFFAOYSA-N
• SMILES:
  ACDLabs 10.04
  OpenEye OEToolkits 1.5.0: [Mg+2]
  CACTVS 3.341: [Mg++]
• Formula: Mg
• Name: MAGNESIUM ION
• DrugBank: DB01378
• PDB chain: 8kdb Chain A Residue 3001

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8kdb Structural basis for dimerization of a paramyxovirus polymerase complex.
• Resolution: 2.7 Å
• Binding residue (original residue number in PDB): Y667 D773
• Binding residue (residue number reindexed from 1): Y633 D739
• Annotation score: 1

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.-

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

External links

• PDB: RCSB:8kdb, PDBe:8kdb, PDBj:8kdb
• PDBsum: 8kdb
• PubMed: 38605025
• UniProt: O89238