Structure of PDB 6rla Chain B Binding Site BS03

Receptor Information

>6rla Chain B (length=2750) Species: 9606 (Homo sapiens)

QGEVTIREALRELDLWGVGAVFTLIDYEDSQSRTMKLIKDWKDIVNQVGD
NRCLLQSLKDSPYYKGFEDKVSIWERKLAELDEYLQNLNHIQRKWVYLEP
IFGRGALPKEQTRFNRVDEDFRSIMTDIKKDNRVTTLTTHAGIRNSLLTI
LDQLQRCQRSLNEFLEEKRSAFPRFYFIGDDDLLEILGQSTNPSVIQSHL
KKLFAGINSVCFDEKSKHITAMKSLEGEVVPFKNKVPLSNNVETWLNDLA
LEMKKTLEQLLKECVTTGRSSQGAVDPSLFPSQILCLAEQIKFTEDVENA
IKDHSLHQIETQLVNKLEQYTNIDTSSEDPGNTESGILELKLKALILDII
HNIDVVKQLNQIQVHTTEDWAWKKQLRFYMKSDHTCCVQMVDSEFQYTYE
YQGNASKLVYTPLTDKCYLTLTQAMKMGLGGNPYGPAGTGKTESVKALGG
LLGRQVLVFNCDEGIDVKSMGRIFVGLVKCGAWGCFDEFNRLEESVLSAV
SMQIQTIQDALKNHRTVCELLGKEVEVNSNSGIFITMNPAGKGYGGRQKL
PDNLKQLFRPVAMSHPDNELIAEVILYSEGFKDAKVLSRKLVAIFNLSRE
LLTPQQHYDWGLRALKTVLRGSGNLLRQLNKSGTTQNANESHIVVQALRL
NTMSKFTFTDCTRFDALIKDVFPGIELKEVEYDELSAALKQVFEEANYEI
IPNQIKKALELYEQLCQRMGVVIVGPSGAGKSTLWRMLRAALCKTGKVVK
QYTMNPKAMPRYQLLGHIDMDTREWSDGVLTNSARQVVREPQDVSSWIIC
DGDIDPEWIESLNSVLDDNRLLTMPSGERIQFGPNVNFVFETHDLSCASP
ATISRMGMIFLSDEETDLNSLIKSWLRNQPAEYRNNLENWIGDYFEKALQ
WVLKQNDYVVETSLVGTVMNGLSHLHGCRDHDEFIINLIRGLGGNLNMKS
RLEFTKEVFHWARESPPDFHKPMDTYYDSTRGRLATYVLKKPEDLTADDF
SNGLTLPVIQTPDMQRGLDYFKPWLSSDTKQPFILVGPEGCGKGMLLRYA
FSQLRSTQIATVHCSAQTTSRHLLQKLSQTCMVISTNTGRVYRPKDCERL
VLYLKDINLPKLDKWGTSTLVAFLQQVLTYQGFYDENLEWVGLENIQIVA
SMSAGGRLGRHKLTTRFTSIVRLCSIDYPEREQLQTIYGAYLEPVLHKNL
KNHSIWGSSSKIYLLAGSMVQVYEQVRAKFTVDDYSHYFFTPCILTQWVL
GLFRYDLEGGSSNHPLDYVLEIVAYEARRLFRDKIVGAKELHLFDIILTS
VFQGDWGSDILDNMSDSFYVTWGARHNSGAPGQPLPPHGKPLGKLNSTDL
KDVIKKGLIHYGRDNQNLDILLFHEVLEYMSRIDRVLSFPGGSLLLAGRS
GVGRRTITSLVSHMHGAVLFSPKISRGYELKQFKNDLKHVLQLAGIEAQQ
VVLLLEDYQFVHPTFLEMINSLLSSGEVPGLYTLEELEPLLLPLKDQASQ
DGFFGPVFNYFTYRIQQNLHIVLIMDSANSNFMINCESNPALHKKCQVLW
MEGWSNSSMKKIPEMLFSEVDPDFLKSFLLIHESCKAYGATPSQYMTFLH
VYSAISSSKKKELLKRQSHLQAGVSKLNEAKALVDELNRKAGEQSVLLET
IKAAEVLINQLDREHKRWNAQVVEITEELATLPKRAQLAAAFITYLSAAP
ESLRKTCLEEWTKSAGLEKFDLRRFLCTESEQLIWKSEGLPSDDLSIENA
LVILQSRVCPFLIDPSSQATEWLKTHLKDSRLEVINQQDSNFITALELAV
RFGKTLIIQEMDGVEPVLYPLLRRDLVAQGPRYVVQIGDKIIDYNEEFRL
FLSTRNPNPFIPPDAASIVTEVNFTTTRSGLRGQLLALTIQHEKPDLEEQ
KTKLLQQEEDKKIQLAKLEESLLETLATSQGNILENKDLIESLNQTKASS
ALIQESLKESYKLQISLDQERDAYLPLAESASKMYFIISDLSKINNMYRF
SLAAFLRLFQRALQNKQDSENTEQRIQSLISSLQHMVYEYICRCLFKADQ
LMFALHFVRGMHPELFQENEWDTFTGVDQLPSWIDQERSWAVATLKIALP
SLYQTLCFEDAALWRTYYNNSMCEQEFPSILAKKVSLFQQILVVQVLRPD
RLQSAMALFACKTLGLKEVSPLPLNLKRLYKETLEIEPILIIISPGADPS
QELQELANAERSGECYHQVAMGQGQADLAIQMLKECARNGDWLCLKNLHL
VVSWLPVLEKELNTLQPKDTFRLWLTAEVHPNFTPILLQSSLKITYESPP
GLKKNLMRTYESWTPEQISKKDNTHRAHALFSLAWFHAACQERRNYIPQG
WTKFYEFSLSDLRAGYNIIDRLFDGAKDVQWEFVHGLLENAIYGGRIDNY
FDLRVLQSYLKQFFIFPYSVSLPQSCSILDYRAVIEKIPEDDKPSFFGLP
ANIARSSQRMISSQVISQLRILGRDREIWSNELSPVLNLWKKLNQNSNLI
HQKVPPPNDRQGSPILSFIILEQFNAIRLVQSVHQSLAALSKVIRGTTLL
SSEVQKLASALLNQKCPLAWQSKWEGPEDPLQYLRGLVARALAIQNWVDK
AEKQALLSETLDLSELFHPDTFLNALRQETARAVGRSVDSLKFVASWKGR
LQEAKLQIKISGLLLEGCSFDGNQLSENQLDSPSVSSVLPCFMGWIPQDA
CGPYSPDECISLPVYTSAERDRVVTNIDVPCGGNQDQWIQCGAALFLKNQ

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: 6rla Chain B Residue 4403

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6rla Structure of the dynein-2 complex and its assembly with intraflagellar transport trains.
• Resolution: 3.9 Å
• Binding residue (original residue number in PDB): S1986 E2095
• Binding residue (residue number reindexed from 1): S732 E841
• Annotation score: 1

Enzymatic activity

• Enzyme Commision number:
  2.1.1.63: methylated-DNA--[protein]-cysteine S-methyltransferase.

Gene Ontology

Molecular Function

• GO:0003677 DNA binding
• GO:0003824 catalytic activity
• GO:0003908 methylated-DNA-[protein]-cysteine S-methyltransferase activity
• GO:0005524 ATP binding
• GO:0008168 methyltransferase activity
• GO:0008569 minus-end-directed microtubule motor activity
• GO:0016887 ATP hydrolysis activity
• GO:0045505 dynein intermediate chain binding
• GO:0046872 metal ion binding
• GO:0051959 dynein light intermediate chain binding

Biological Process

• GO:0006259 DNA metabolic process
• GO:0006281 DNA repair
• GO:0007018 microtubule-based movement
• GO:0030030 cell projection organization
• GO:0032259 methylation

Cellular Component

• GO:0005634 nucleus
• GO:0005737 cytoplasm
• GO:0005856 cytoskeleton
• GO:0005874 microtubule
• GO:0005886 plasma membrane
• GO:0030286 dynein complex

External links

• PDB: RCSB:6rla, PDBe:6rla, PDBj:6rla
• PDBsum: 6rla
• PubMed: 31451806
• UniProt: B0I1S0;
  E5BBQ0