Structure of PDB 5jpt Chain B Binding Site BS01

Receptor Information

>5jpt Chain B (length=741) Species: 559292 (Saccharomyces cerevisiae S288C) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]

SKRRFSSEHPDPVETSIPEQAAEIAEELSKQHPLPSEEPLVHHDAGEFKG
LQRHHTSAEEAQKLEDGKINPFTGREFTPKYVDILKIRRELPVHAQRDEF
LKLYQNNQIMVFVGETGSGKTTQIPQFVLFDEMPHLENTQVACTQPRRVA
AMSVAQRVAEEMDVKLGEEVGYSIRFENKTSNKTILKYMTDGMLLREAME
DHDLSRYSCIILDEAHERTLATDILMGLLKQVVKRRPDLKIIIMSATLDA
EKFQRYFNDAPLLAVPGRTYPVELYYTPEFQRDYLDSAIRTVLQIHATEE
AGDILLFLTGEDEIEDAVRKISLEGDQLVREEGCGPLSVYPLYGSLPPHQ
QQRIFEPAPESHNGRPGRKVVISTNIAETSLTIDGIVYVVDPGFSKQKVY
NPRIRVESLLVSPISKASAQQRAGRAGRTRPGKCFRLYTEEAFQKELIEQ
SYPEILRSNLSSTVLELKKLGIDDLVHFDFMDPPAPETMMRALEELNYLA
CLDDEGNLTPLGRLASQFPLDPMLAVMLIGSFEFQCSQEILTIVAMLSVP
NVFIRPTKDKKRADDAKNIFAHPDGDHITLLNVYHAFKSDEAYEYGIHKW
CRDHYLNYRSLSAADNIRSQLERLMNRYNLELNTTDYESPKYFDNIRKAL
ASGFFMQVAKKRGYITVKDNQDVLIHPSTVLGHDAEWVIYNEFVLTSKNY
IRTVTSVRPEWLIEIAPAYYDLSNFQKGDVKLSLERIKEKV

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

Software	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

PDB chain

5jpt Chain B Residue 801 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]

Receptor-Ligand Complex Structure

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Structure summary

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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)	T118 G119 S120 G121 K122 T123 T124 S155 V156 R159 F357 T384 D386 R430
Binding residue (residue number reindexed from 1)	T116 G117 S118 G119 K120 T121 T122 S153 V154 R157 F355 T382 D384 R428
Annotation score	2

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

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Molecular Function

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Cellular Component

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)

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