Structure of PDB 8kdc Chain A Binding Site BS01

Receptor Information

>8kdc Chain A (length=2114) Species: 11216 (Human respirovirus 3)

VSDILYPECHLNSPIVKGKIAQLHTIMSLPQPYDMDDDSILVITRQKIKL
NKLDKRQRSIRRLKLILTEKVNDLGKYTFIRYPEMSKEMFKLYIPGINSK
VTELLLKADRTYSQMTDGLRDLWINVLSKLASKNDGSNYDLNEEINNISK
VHTTYKSDKWYNPFKTWFTIKYDMRRLQKARNEITFNVGKDYNLLEDQKN
FLLIHPELVLILDKQNYNGYLITPELVLMYCDVVEGRWNISACAKLDPKL
QSMYQKGNNLWEVIDKLFPIMGEKTFDVISLLEPLALSLIQTHDPVKQLR
GAFLNHVLSEMELIFESGESIREFLSVDYIDKILDIFNESTIDEIAEIFS
FFRTFGHPPLEASIAAEKVRKYMYIEKQLKFDTVNKCHAIFCTIIINGYR
ERHGGQWPPVTLPDHAHEFIINAYGSNSAISYENAVDYYQSFIGIKFNKF
IEPQLDEDLTIYMKDKALSPKKSNWDTVYPASNLLYRTNASNESRRLVEV
FIADSKFDPHQILDYVESGDWLDDPEFNISYSLKEKEIKQEGRLFAKMTY
KMRATQVLSETLLANNIGKFFQENGMVKGEIELLKRLTTISISGVPRYNE
SKKFEFKSTDIYNDGYETVSCFLTTDLKKYCLNWRYESTALFGETCNQIF
GLNKLFNWLHPRLEGSTIYVGDPYCPPSDKEHISLEDHPDSGFYVHNPRG
GIEGFCQKLWTLISISAIHLAAVRIGVRVTAMVQGDNQAIAVTTRVPNNY
DYRIKKEIVYKDVVRFFDSLREVMDDLGHELKLNETIISSKMFIYSKRIY
YDGRILPQALKALSRCVFWSETVIDETRSASSNLATSFAKAIENGYSPVL
GYACSIFKNIQQLYIALGMNINPTITQNIKDQYFKNSNWMQYASLIPASV
GGFNYMAMSRCFVRNIGDPSVAALADIKRFIKANLLDRSVLYRIMNQEPG
ESSFLDWASDPYSCNLPQSQNITTMIKNITARNVLQDSPNPLLSGLFTNT
MIEEDEELAEFLMDRKVILPRVAHDILDNSLTGIRNAIAGMLDTTKSLIR
VGINRGGLTYSLLRKISNYDLVQYETLSRTLRLIVSDKIRYEDMCSVDLA
IALRQKMWIHLSGGRMISGLETPDPLELLSGVVITGSEHCKICYSSDGTN
PYTWMYLPGNIKIGSAETGVSSLRVPYFGSVTDERSEAQLGYIKNLSKPA
KAAIRIAMIYTWAFGNDEISWMEASQIAQTRANFTLDSLKILTPVATSTN
LSHRKFSSTSLIRVSRFITMSNDNMSIKEANETKDTNLIYQQIMLTGLSV
FEYLFRLKETTGHNPIVMHLHIEDECCIKESFNDEHINPESTLELIRYPE
SNEFIYDKDPLKDVDLSKLMVIKDHSYTIDMNYWDDTDIIHAISICTAIT
IADTMSQLDRDNLKEIIVIANDDDINSLITEFLTLDILVFLKTFGGLLVN
QFAYTLYSLKIEGRDLIWDYIMRTLRDTSHSILKVLSNALSHPKVFKRFW
DCGVLNPIYGPNTASQDQIKLALSICEYALDLFMREWLNGVSLEIYICDS
DMEVANDRKQAFISRHLSFVCCLAEIASFGPNLLNLTYLERLDLLKQYLE
LNIKEDPTLKYVQISGLLIKSFPSTVTYVRKTAIKYLRIRGISPPEVNIV
KTINDNCNKDNKGNKINNFWGLALKNYQVLKIRSILPQGGNYLSHQLRLF
GINSTSCLKALELSQILMKEVNKDKDRLFLGEGAGAMLACYDATLGPAIN
YYNSGLNITDVIGQRELKIFPSEVSLVGKKLGNVTQILNRVKVLFNGNPN
STWIGNMECESLIWSELNDKSIGLVHCDMEGAIGKSEETVLHEHYSVIRI
TYLIGDDDVVLVSKIIPTITPNWSRILYLYKLYWKDVSIISLKTSNPAST
ELYLISKDAYCTIMEPSEVVLSKLKRLSLLEENNLLKWIILSKKRNNEWL
HHEIKEGERDYGVMRPYHMALQIFGFQINLNHLAKEFLSTPDLTNINNII
QSFQRTIKDVLFEWININKGKLRLLSRRLVLSWISLSLSTRLLTGRFPDE
KFEHRAQTGYVSLADTDLESLKLLSKNIIKNYRECIGSISYWFLTKEVKI
LMKLIGGAKLLGIP

Ligand information

• Ligand ID: ZN
• InChI: InChI=1S/Zn/q+2
• InChIKey: PTFCDOFLOPIGGS-UHFFFAOYSA-N
• SMILES:
  CACTVS 3.341: [Zn++]
  ACDLabs 10.04
  OpenEye OEToolkits 1.5.0: [Zn+2]
• Formula: Zn
• Name: ZINC ION
• ChEMBL: CHEMBL1236970
• DrugBank: DB14532
• PDB chain: 8kdc Chain A Residue 3002

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8kdc Structural basis for dimerization of a paramyxovirus polymerase complex.
• Resolution: 3.3 Å
• Binding residue (original residue number in PDB): C1177 H1364 H1366
• Binding residue (residue number reindexed from 1): C1140 H1319 H1321
• 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:8kdc, PDBe:8kdc, PDBj:8kdc
• PDBsum: 8kdc
• PubMed: 38605025
• UniProt: O89238