Structure of PDB 6sc2 Chain A Binding Site BS04

Receptor Information
>6sc2 Chain A (length=3914) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KLFIFTTTQNYFGLMSELWDQPLLCNCLEINNFLDDGNQMLLRVQRSDAG
ISFSNTIEFGDTKDKVLVFFKLRPEVITDENLHDNILVSSMLESPISSLY
QAVRQVFAPMLLKDQEWSRNFDPKLQNLLSELEAGLGIVLRRSKERANYF
KELFETIAREFYNLDSLSLLEVVDLVETTQDVVDDVWRQTEHDHYPESRM
LHLLDIIGGSFGRFVQKKLGTLNLWEDPYYLVKESLKAGISICEQWVIVC
NHLTGQVWQRYVPHPWKNEKYFPETLDKLGKRLEEVLAIRTIHEKFLYFL
PASEEKIICLTRVFEPFTGLNPVQYNPYTEPLWKAAVSQYEKIIAPAEQK
IAGKLKNYISEIQDSPQQLLQAFLKYKELVKRPTISKELMLERETLLARL
VDSIKDFRLDFENRSEVVNSIVWVRQLELKVDDTIKIAEALLSDLPGFRC
FHQSAKDLLDQLKLYEQEQFDDWSRDIQSGLSDSRSGLCIEASSRIMELD
SNDGLLKVHYSDRLVILLREVRQLSALGFVIPAKIQQVANIAQKFCKQAI
ILKQVAHFYNSIDQQMIQSQRPMMLQSALAFEQIIKNSKAGSGGKSQITW
DNPKELEGYIQKLQNAAERLATENRKLRKWHTTFCEKVVVLMNIDLLRQQ
QRWKDGLQELRTGLATVEAQGFQASDMHAWKQHWNHQLYKALEHQYQMGL
EALNENLPEINIDLTYKQGRLQFRPPFEEIRAKYYREMKRFIGIPNQFKG
VGEAGDESIFSIMIDRNASGFLTIFSKAEDLFRRLSAVLHQHKEWIVIGQ
VDMEALVEKHLFTVHDWEKNFKALKIKGKEVERLPSAVKVDCLNINCNPV
KTVIDDLIQKLFDLLVLSLKKSIQAHLHEIDTFVTEAMEVLTIMPQSVEE
IGDANLQYSKLQERKPEILPLFQEAEDKNRLLRTVAGGGLETISNLKAKW
DKFELAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAATLIDYEDSQSRTMK
LIKDWKDIVNQVGDNRCLLQSLKDSPYYKGFEDKVSIWERKLAELDEYLQ
NLNHIQRKWVYLEPIFGRGALPKEQTRFNRVDEDFRSIMTDIKKDNRVTT
LTTHAGIRNSLLTILDQLQRCQRSLNEFLEEKRSAFPRFYFIGDDDLLEI
LGQSTNPSVIQSHLKKLFAGINSVCFDEKSKHITAMKSLEGEVVPFKNKV
PLSNNVETWLNDLALEMKKTLEQLLKECVTTGRSSQGAVDPSLFPSQILC
LAEQIKFTEDVENAIKDHSLHQIETQLVNKLEQYTNIDTSSEDPGNTESG
ILELKLKALILDIIHNIDVVKQLNQIQVHTTEDWAWKKQLRFYMKSDHTC
CVQMVDSEFQYTYEYQGNASKLVYTPLTDKCYLTLTQAMKMGLGGNPYGP
AGTGKTESVKALGGLLGRQVLVFNCDEGIDVKSMGRIFVGLVKCGAWGCF
DEFNRLEESVLSAVSMQIQTIQDALKNHRTVCELLGKEVEVNSNSGIFIT
MNPAGKGYGGRQKLPDNLKQLFRPVAMSHPDNELIAEVILYSEGFKDAKV
LSRKLVAIFNLSRELLTPQQHYDWGLRALKTVLRGSGNLLRQLNKSGTTQ
NANESHIVVQALRLNTMSKFTFTDCTRFDALIKDVFPGIELKEVEYDELS
AALKQVFEEANYEIIPNQIKKALELYEQLCQRMGVVIVGPSGAGKSTLWR
MLRAALCKTGKVVKQYTMNPKAMPRYQLLGHIDMDTREWSDGVLTNSARQ
VVREPQDVSSWIICDGDIDPEWIESLNSVLDDNRLLTMPSGERIQFGPNV
NFVFETHDLSCASPATISRMGMIFLSDEETDLNSLIKSWLRNQPAEYRNN
LENWIGDYFEKALQWVLKQNDYVVETSLVGTVMNGLSHLHGCRDHDEFII
NLIRGLGGNLNMKSRLEFTKEVFHWARESPPDFHKPMDTYYDSTRGRLAT
YVLKKPEDLTADDFSNGLTLPVIQTPDMQRGLDYFKPWLSSDTKQPFILV
GPEGCGKGMLLRYAFSQLRSTQIATVHCSAQTTSRHLLQKLSQTCMVIST
NTGRVYRPKDCERLVLYLKDINLPKLDKWGTSTLVAFLQQVLTYQGFYDE
NLEWVGLENIQIVASMSAGGRLGRHKLTTRFTSIVRLCSIDYPEREQLQT
IYGAYLEPVLHKNLKNHSIWGSSSKIYLLAGSMVQVYEQVRAKFTVDDYS
HYFFTPCILTQWVLGLFRYDLEGGSSNHPLDYVLEIVAYEARRLFRDKIV
GAKELHLFDIILTSVFQGDWGSDILDNMSDSFYVTWGARHNSGAPGQPLP
PHGKPLGKLNSTDLKDVIKKGLIHYGRDNQNLDILLFHEVLEYMSRIDRV
LSFPGGSLLLAGRSGVGRRTITSLVSHMHGAVLFSPKISRGYELKQFKND
LKHVLQLAGIEAQQVVLLLEDYQFVHPTFLEMINSLLSSGEVPGLYTLEE
LEPLLLPLKDQASQDGFFGPVFNYFTYRIQQNLHIVLIMDSANSNFMINC
ESNPALHKKCQVLWMEGWSNSSMKKIPEMLFSEVDPDFLKSFLLIHESCK
AYGATPSQYMTFLHVYSAISSSKKKELLKRQSHLQAGVSKLNEAKALVDE
LNRKAGEQSVLLETIKAAEVLINQLDREHKRWNAQVVEITEELATLPKRA
QLAAAFITYLSAAPESLRKTCLEEWTKSAGLEKFDLRRFLCTESEQLIWK
SEGLPSDDLSIENALVILQSRVCPFLIDPSSQATEWLKTHLKDSRLEVIN
QQDSNFITALELAVRFGKTLIIQEMDGVEPVLYPLLRRDLVAQGPRYVVQ
IGDKIIDYNEEFRLFLSTRNPNPFIPPDAASIVTEVNFTTTRSGLRGQLL
ALTIQHEKPDLEEQKTKLLQQEEDKKIQLAKLEESLLETLATSQGNILEN
KDLIESLNQTKASSALIQESLKESYKLQISLDQERDAYLPLAESASKMYF
IISDLSKINNMYRFSLAAFLRLFQRALQNKQDSENTEQRIQSLISSLQHM
VYEYICRCLFKADQLMFALHFVRGMHPELFQENEWDTFTGVDQLPSWIDQ
ERSWAVATLKIALPSLYQTLCFEDAALWRTYYNNSMCEQEFPSILAKKVS
LFQQILVVQVLRPDRLQSAMALFACKTLGLKEVSPLPLNLKRLYKETLEI
EPILIIISPGADPSQELQELANAERSGECYHQVAMGQGQADLAIQMLKEC
ARNGDWLCLKNLHLVVSWLPVLEKELNTLQPKDTFRLWLTAEVHPNFTPI
LLQSSLKITYESPPGLKKNLMRTYESWTPEQISKKDNTHRAHALFSLAWF
HAACQERRNYIPQGWTKFYEFSLSDLRAGYNIIDRLFDGAKDVQWEFVHG
LLENAIYGGRIDNYFDLRVLQSYLKQFFIFPYSVSLPQSCSILDYRAVIE
KIPEDDKPSFFGLPANIARSSQRMISSQVISQLRILGRDREIWSNELSPV
LNLWKKLNQNSNLIHQKVPPPNDRQGSPILSFIILEQFNAIRLVQSVHQS
LAALSKVIRGTTLLSSEVQKLASALLNQKCPLAWQSKWEGPEDPLQYLRG
LVARALAIQNWVDKAEKQALLSETLDLSELFHPDTFLNALRQETARAVGR
SVDSLKFVASWKGRLQEAKLQIKISGLLLEGCSFDGNQLSENQLDSPSVS
SVLPCFMGWIPQDACGPYSPDECISLPVYTSAERDRVVTNIDVPCGGNQD
QWIQCGAALFLKNQ
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 chain6sc2 Chain A Residue 4405 [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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PDB6sc2 Structure of the dynein-2 complex and its assembly with intraflagellar transport trains.
Resolution3.9 Å
Binding residue
(original residue number in PDB)		L2628 V2659 G2660 R2661
Binding residue
(residue number reindexed from 1)		L2535 V2566 G2567 R2568
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:6sc2, PDBe:6sc2, PDBj:6sc2
PDBsum6sc2
PubMed31451806
UniProtB0I1S0;
E5BBQ0

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