Structure of PDB 7d4i Chain RZ Binding Site BS01

Receptor Information
>7d4i Chain RZ (length=838) Species: 559292 (Saccharomyces cerevisiae S288C) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
AFYVEVSRSDEIQKARIQLPVFGEEHKIMEAIHHNDVVIICGETGSGKTT
QVPQFLYEAGFGAEDSPDYPGMVGITQPRRVAAVSMAERVANELGDHGHK
VGYQIRFDSTAKEDTKVKFMTDGVLLREMMHDFKLTKYSSIIIDEAHERN
INTDILIGMLSRCVRLRAKLHKENPIEHKKLKLIIMSATLRVSDFSENKT
LFPIAPPVLQVDARQFPVSIHFNRRTAFNYTDEAFRKTCKIHQKLPPGAI
LVFLTGQQEITHMVKRLRKEFPFKKNSKYNKDLETPVSKMGINSKTTDLE
AEDIDFSVQVIDQDKFKSAIRYEEEEEEGFEEVLTEGQTANDPLYVLPLY
SLLPTKEQMRVFQKPPQGSRLCIVATNVAETSLTIPGVRYVVDSGRSKER
KYNESNGVQSFEVGWVSKASANQRSGRAGRTGPGHCYRLYSSAVFEHDFE
QFKPEILRMPVESIVLQMKSMAIHNIINFPFPTPPDRVALSKAIQLLQYL
GALDNKEMITEDGKKMSLFPLSPRFSKMLLVSDEKACLPYIVAIVSALSV
GDPFINEFELGPELKKELRSKFYKSRSQFSKLDKFSDVFRLLSVVSAMDY
VPKEQKEIFMKKNFLRGKLMEEIVKLRKQLMYIIKSNTSKENIAVVIRNE
DLKSDIPSVIQIKLLKQMICAGFVDHVAVRADVLFPDDAKITNRTSIINI
PYIPVLATRTPNIEDCFVYIHPTSILNNLGEMPPKYMLYYSLHLGGNNKT
RMNTLCDIASTPLANIARKGLLLTYSKPLTGQGLKTVNLSPTERYCYVVP
RFGSTVDNDLKIGWDLNPIAVHQKKQKGQWTVIKFITR
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 chain7d4i Chain RZ Residue 1301 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB7d4i Cryo-EM structure of 90S small ribosomal precursors complex with Dhr1
Resolution4.0 Å
Binding residue
(original residue number in PDB)		E415 T416 G417 S418 G419 K420 T421 T422 M458 E460 R461 F747 T769 P771
Binding residue
(residue number reindexed from 1)		E43 T44 G45 S46 G47 K48 T49 T50 M86 E88 R89 F362 T384 P386
Annotation score5
Enzymatic activity
Enzyme Commision number 3.6.4.13: RNA helicase.
Gene Ontology
Molecular Function
GO:0003676 nucleic acid binding
GO:0003723 RNA binding
GO:0003724 RNA helicase activity
GO:0004386 helicase activity
GO:0005515 protein binding
GO:0005524 ATP binding
GO:0008186 ATP-dependent activity, acting on RNA
GO:0016787 hydrolase activity
GO:0016887 ATP hydrolysis activity
Biological Process
GO:0000462 maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
GO:0006364 rRNA processing
GO:0006396 RNA processing
GO:0022613 ribonucleoprotein complex biogenesis
GO:0030490 maturation of SSU-rRNA
GO:0042254 ribosome biogenesis
Cellular Component
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005730 nucleolus
GO:0005739 mitochondrion
GO:0030686 90S preribosome
GO:0032040 small-subunit processome
GO:1990904 ribonucleoprotein complex

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:7d4i, PDBe:7d4i, PDBj:7d4i
PDBsum7d4i
PubMed
UniProtQ04217|DHR1_YEAST Probable ATP-dependent RNA helicase DHR1 (Gene Name=ECM16)

[Back to BioLiP]