Structure of PDB 7bdj Chain B Binding Site BS02

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 2202

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): F1328 Q1332 T1352 G1353 G1355 K1356 T1357 I1358 D1454 E1455 N1655 P1694
• Binding residue (residue number reindexed from 1): F923 Q927 T947 G948 G950 K951 T952 I953 D1049 E1050 N1250 P1289
• 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)