Structure of PDB 6rla Chain A Binding Site BS04

Receptor Information
>6rla Chain A (length=2750) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
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 IDADP
InChIInChI=1S/C10H15N5O10P2/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(24-10)1-23-27(21,22)25-26(18,19)20/h2-4,6-7,10,16-17H,1H2,(H,21,22)(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1
InChIKeyXTWYTFMLZFPYCI-KQYNXXCUSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)OP(=O)(O)O)O)O)N
CACTVS 3.341Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
ACDLabs 10.04O=P(O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
CACTVS 3.341Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@@](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)O)O)N
FormulaC10 H15 N5 O10 P2
NameADENOSINE-5'-DIPHOSPHATE
ChEMBLCHEMBL14830
DrugBankDB16833
ZINCZINC000012360703
PDB chain6rla Chain A Residue 4404 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB6rla Structure of the dynein-2 complex and its assembly with intraflagellar transport trains.
Resolution3.9 Å
Binding residue
(original residue number in PDB)		M2268 G2294 C2295 G2296 K2297 G2298 M2299 K2359 I2441 T2500
Binding residue
(residue number reindexed from 1)		M1014 G1040 C1041 G1042 K1043 G1044 M1045 K1105 I1187 T1246
Annotation score1
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

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:6rla, PDBe:6rla, PDBj:6rla
PDBsum6rla
PubMed31451806
UniProtB0I1S0;
E5BBQ0

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