Structure of PDB 5jpt Chain A Binding Site BS01

Receptor Information

>5jpt Chain A (length=745) Species: 559292 (Saccharomyces cerevisiae S288C)

SKRRFSSEHPDPVETSIPEQAAEIAEELSKQHPLPSEEPLVHHDAGEFKG
LQRHHTSAEEAQKLEDGKINPFTGREFTPKYVDILKIRRELPVHAQRDEF
LKLYQNNQIMVFVGETGSGKTTQIPQFVLFDEMPHLENTQVACTQPRRVA
AMSVAQRVAEEMDVKLGEEVGYSIRFENKTSNKTILKYMTDGMLLREAME
DHDLSRYSCIILDEAHERTLATDILMGLLKQVVKRRPDLKIIIMSATLDA
EKFQRYFNDAPLLAVPGRTYPVELYYTPEFQRDYLDSAIRTVLQIHATEE
AGDILLFLTGEDEIEDAVRKISLEGDQLVREEGCGPLSVYPLYGSLPPHQ
QQRIFEPAPESHNGRPGRKVVISTNIAETSLTIDGIVYVVDPGFSKQKVY
NPRIRVESLLVSPISKASAQQRAGRAGRTRPGKCFRLYTEEAFQKELIEQ
SYPEILRSNLSSTVLELKKLGIDDLVHFDFMDPPAPETMMRALEELNYLA
CLDDEGNLTPLGRLASQFPLDPMLAVMLIGSFEFQCSQEILTIVAMLSVP
NVFIRPTKDKKRADDAKNIFAHPDGDHITLLNVYHAFKSDEAYEYGIHKW
CRDHYLNYRSLSAADNIRSQLERLMNRYNLELNTTDYESPKYFDNIRKAL
ASGFFMQVAKKRSGGYITVKDNQDVLIHPSTVLGHDAEWVIYNEFVLTSK
NYIRTVTSVRPEWLIEIAPAYYDLSNFQKGDVKLSLERIKEKVDR

Ligand information

• Ligand ID: CDP
• InChI: InChI=1S/C9H15N3O11P2/c10-5-1-2-12(9(15)11-5)8-7(14)6(13)4(22-8)3-21-25(19,20)23-24(16,17)18/h1-2,4,6-8,13-14H,3H2,(H,19,20)(H2,10,11,15)(H2,16,17,18)/t4-,6-,7-,8-/m1/s1
• InChIKey: ZWIADYZPOWUWEW-XVFCMESISA-N
• SMILES:
  OpenEye OEToolkits 1.5.0: C1=CN(C(=O)N=C1N)C2C(C(C(O2)COP(=O)(O)OP(=O)(O)O)O)O
  CACTVS 3.341: NC1=NC(=O)N(C=C1)[C@@H]2O[C@H](CO[P@](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]2O
  ACDLabs 10.04: O=P(O)(O)OP(=O)(O)OCC2OC(N1C(=O)N=C(N)C=C1)C(O)C2O
  OpenEye OEToolkits 1.5.0: C1=CN(C(=O)N=C1N)[C@H]2[C@@H]([C@@H]([C@H](O2)CO[P@@](=O)(O)OP(=O)(O)O)O)O
  CACTVS 3.341: NC1=NC(=O)N(C=C1)[CH]2O[CH](CO[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]2O
• Formula: C9 H15 N3 O11 P2
• Name: CYTIDINE-5'-DIPHOSPHATE
• ChEMBL: CHEMBL425252
• DrugBank: DB04555
• ZINC: ZINC000008215624
• PDB chain: 5jpt Chain A Residue 801

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5jpt Functional link between DEAH/RHA helicase Prp43 activation and ATP base binding.
• Resolution: 2.935 Å
• Binding residue (original residue number in PDB): G119 G121 K122 T123 T124 S155 V156 R159 F357 T384 D386 R430
• Binding residue (residue number reindexed from 1): G117 G119 K120 T121 T122 S153 V154 R157 F355 T382 D384 R428
• Annotation score: 2
• Binding affinity: PDBbind-CN: -logKd/Ki=4.60,Kd>25uM

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:0003729 mRNA binding
• 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:0000390 spliceosomal complex disassembly
• GO:0000462 maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
• GO:0000463 maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
• GO:0000466 maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
• GO:0006364 rRNA processing
• GO:0006396 RNA processing
• GO:0006397 mRNA processing
• GO:0008380 RNA splicing
• GO:0022613 ribonucleoprotein complex biogenesis
• GO:0030490 maturation of SSU-rRNA
• GO:0042273 ribosomal large subunit biogenesis

Cellular Component

• GO:0005634 nucleus
• GO:0005681 spliceosomal complex
• GO:0005730 nucleolus
• GO:0005739 mitochondrion
• GO:0030686 90S preribosome
• GO:0032040 small-subunit processome
• GO:0071014 post-mRNA release spliceosomal complex
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:5jpt, PDBe:5jpt, PDBj:5jpt
• PDBsum: 5jpt
• PubMed: 28180308
• UniProt: P53131|PRP43_YEAST Pre-mRNA-splicing factor ATP-dependent RNA helicase PRP43 (Gene Name=PRP43)