Structure of PDB 7bdj Chain B Binding Site BS01

Receptor Information

>7bdj Chain B (length=1722) Species: 9606 (Homo sapiens)

LAPRQVLDLEDLVFTQGSHFMANKRCQLPDGSFRRQRKGYEEVHVPALKP
KPFGSEEQLLPVEKLPKYAQAGFEGFKTLNRIQSKLYRAALETDENLLLC
APTGAGKTNVALMCMLREIGKHINMDGTINVDDFKIIYIAPMRSLVQEMV
GSFGKRLATYGITVAELTGDHQEEISATQIIVCTPEKWDIITRKGGERTY
TQLVRLIILDEIHLLHDDRGPVLEALVARAIRNIEMTQEDVRLIGLSATL
PNYEDVATFLRVDPAKGLFYFDNSFRPVPLEQTYVGITEKKAIKRFQIMN
EIVYEKIMEHAGKNQVLVFVHSRKETGKTARAIRDMCLEKDTLGLFLREG
SASTEVLRTEAEQCKNLELKDLLPYGFAIHHAGMTRVDRTLVEDLFADKH
IQVLVSTATLAWGVNLPAHTVIIKGTQVYSPEKGRWTELGALDILQMLGR
AGRPQYDTKGEGILITSHGELQYYLSLLNQQLPIESQMVSKLPDMLNAEI
VLGNVQNAKDAVNWLGYAYLYIRMLRSPTLYGISHDDLKGDPLLDQRRLD
LVHTAALMLDKNNLVKYDKKTGNFQVTELGRIASHYYITNDTVQTYNQLL
KPTLSEIELFRVFSLSSEFKNITVREEEKLELQKLLERVPIPVKESIEEP
SAKINVLLQAFISQLKLEGFALMADMVYVTQSAGRLMRAIFEIVLNRGWA
QLTDKTLNLCKMIDKRMWQSMCPLRQFRKLPEEVVKKIEKKNFPFERLYD
LNHNEIGELIRMPKMGKTIHKYVHLFPKLELSVHLQPITRSTLKVELTIT
PDFQWDEKVHGSSEAFWILVEDVDSEVILHHEYFLLKAKYAQDEHLITFF
VPVFEPLPPQYFIRVVSDRWLSCETQLPVSFRHLILPEKYPPPTELLDLQ
PLPVSALRNSAFESLYQDKFPFFNPIQTQVFNTVYNSDDNVFVGAPTGSG
KTICAEFAILRMLLQSSEGRCVYITPMEALAEQVYMDWYEKFQDRLNKKV
VLLTGETSTDLKLLGKGNIIISTPEKWDILSRRWKQRKNVQNINLFVVDE
VHLIGGENGPVLEVICSRMRYISSQIERPIRIVALSSSLSNAKDVAHWLG
CSATSTFNFHPNVRPVPLELHIQGFNISHTQTRLLSMAKPVYHAITKHSP
KKPVIVFVPSRKQTRLTAIDILTTCAADIQRQRFLHCTEKDLIPYLEKLS
DSTLKETLLNGVGYLHEGLSPMERRLVEQLFSSGAIQVVVASRSLCWGMN
VAAHLVIIMDTQYYNGKIHAYVDYPIYDVLQMVGHANRPLQDDEGRCVIM
CQGSKKDFFKKFLYEPLPVESHLDHCMHDHFNAEIVTKTIENKQDAVDYL
TWTFLYRRMTQNPNYYNLQGISHRHLSDHLSELVEQTLSDLEQSKCISIE
DEMDVAPLNLGMIAAYYYINYTTIELFSMSLNAKTKVRGLIEIISNAAEY
ENIPIRHHEDNLLRQLAQKVPHKLNNPKFNDPHVKTNLLLQAHLSRMQLS
AELQSDTEEILSKAIRLIQACVDVLSSNGWLSPALAAMELAQMVTQAMWS
KDSYLKQLPHFTSEHIKRCTDKGVESVFDIMEMEDEERNALLQLTDSQIA
DVARFCNRYPNIELSYEVVDKDSIRSGGPVVVLVQLEREEEVTGPVIAPL
FPQKREEGWWVVIGDAKSNSLISIKRLTLQQKAKVKLDFVAPATGAHNYT
LYFMSDAYMGCDQEYKFSVDVK

Ligand information

• Ligand ID: TGB
• InChI: InChI=1S/C18H23N6O13P3S/c1-20-10-5-3-2-4-9(10)18(26)35-14-11(6-33-38(27,28)36-39(29,30)37-40(31,32)41)34-17(13(14)25)24-8-23-12-15(19)21-7-22-16(12)24/h2-5,7-8,11,13-14,17,20,25H,6H2,1H3,(H,27,28)(H,29,30)(H2,19,21,22)(H2,31,32,41)/t11-,13-,14-,17-/m1/s1
• InChIKey: MAHRZZRRCDZDJN-LSCFUAHRSA-N
• SMILES:
  OpenEye OEToolkits 2.0.7: CNc1ccccc1C(=O)O[C@@H]2[C@H](O[C@H]([C@@H]2O)n3cnc4c3ncnc4N)COP(=O)(O)OP(=O)(O)OP(=O)(O)S
  CACTVS 3.385: CNc1ccccc1C(=O)O[CH]2[CH](O)[CH](O[CH]2CO[P](O)(=O)O[P](O)(=O)O[P](O)(S)=O)n3cnc4c(N)ncnc34
  CACTVS 3.385: CNc1ccccc1C(=O)O[C@H]2[C@@H](O)[C@@H](O[C@@H]2CO[P](O)(=O)O[P](O)(=O)O[P](O)(S)=O)n3cnc4c(N)ncnc34
  OpenEye OEToolkits 2.0.7: CNc1ccccc1C(=O)OC2C(OC(C2O)n3cnc4c3ncnc4N)COP(=O)(O)OP(=O)(O)OP(=O)(O)S
• Formula: C18 H23 N6 O13 P3 S
• Name: [[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3-[2-(methylamino)phenyl]carbonyloxy-4-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-sulfanyl-phosphinic acid
• PDB chain: 7bdj Chain B Residue 2201

Receptor-Ligand Complex Structure

Structure summary

• PDB: 7bdj Long-range allostery mediates cooperative adenine nucleotide binding by the Ski2-like RNA helicase Brr2.
• Resolution: 2.59 Å
• Binding residue (original residue number in PDB): F478 L481 N482 Q485 T505 G506 G508 K509 T510 N511 D615 E616
• Binding residue (residue number reindexed from 1): F76 L79 N80 Q83 T103 G104 G106 K107 T108 N109 D210 E211
• Annotation score: 2

Enzymatic activity

• Enzyme Commision number: 3.6.4.13: RNA helicase.

Gene Ontology

Molecular Function

• GO:0003676 nucleic acid binding
• GO:0005524 ATP binding

External links

• PDB: RCSB:7bdj, PDBe:7bdj, PDBj:7bdj
• PDBsum: 7bdj
• PubMed: 34048711
• UniProt: O75643|U520_HUMAN U5 small nuclear ribonucleoprotein 200 kDa helicase (Gene Name=SNRNP200)