Structure of PDB 3kx2 Chain A Binding Site BS01

Receptor Information

>3kx2 Chain A (length=755) Species: 559292 (Saccharomyces cerevisiae S288C) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]

MGSKRRFSSEHPDPVETSIPEQAAEIAEELSKQHPLPSEEPLVHHDAGEF
KGLQRHHTSAEEAQKLEDGKINPFTGREFTPKYVDILKIRRELPVHAQRD
EFLKLYQNNQIMVFVGETGSGKTTQIPQFVLFDEMPHLENTQVACTQPRR
VAAMSVAQRVAEEMDVKLGEEVGYSIRFENKTSNKTILKYMTDGMLLREA
MEDHDLSRYSCIILDEAHERTLATDILMGLLKQVVKRRPDLKIIIMSATL
DAEKFQRYFNDAPLLAVPGRTYPVELYYTPEFQRDYLDSAIRTVLQIHAT
EEAGDILLFLTGEDEIEDAVRKISLEGDQLVREEGCGPLSVYPLYGSLPP
HQQQRIFEPAPESHNGRPGRKVVISTNIAETSLTIDGIVYVVDPGFSKQK
VYNPRIRVESLLVSPISKASAQQRAGRAGRTRPGKCFRLYTEEAFQKELI
EQSYPEILRSNLSSTVLELKKLGIDDLVHFDFMDPPAPETMMRALEELNY
LACLDDEGNLTPLGRLASQFPLDPMLAVMLIGSFEFQCSQEILTIVAMLS
VPNVFIRPTKDKKRADDAKNIFAHPDGDHITLLNVYHAFKSDEAYEYGIH
KWCRDHYLNYRSLSAADNIRSQLERLMNRYNLELNTTDYESPKYFDNIRK
ALASGFFMQVAKKRSGAKGYITVKDNQDVLIHPSTVLGHDAEWVIYNEFV
LTSKNYIRTVTSVRPEWLIEIAPAYYDLSNFQKGDVKLSLERIKEKVDRL
NELKQ

Ligand information

Ligand ID

ADP

InChI

InChI=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

InChIKey

XTWYTFMLZFPYCI-KQYNXXCUSA-N

SMILES

Software	SMILES
OpenEye OEToolkits 1.5.0	c1nc(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 3.341	Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
ACDLabs 10.04	O=P(O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
CACTVS 3.341	Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@@](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
OpenEye OEToolkits 1.5.0	c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)O)O)N

Formula

C10 H15 N5 O10 P2

Name

ADENOSINE-5'-DIPHOSPHATE

PDB chain

3kx2 Chain A Residue 1000 [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	3kx2 Structural basis for the function of DEAH helicases
Resolution	2.2 Å
Binding residue (original residue number in PDB)	T118 G119 G121 K122 T123 T124 R159 F357 D386 R430
Binding residue (residue number reindexed from 1)	T118 G119 G121 K122 T123 T124 R159 F357 D386 R430
Annotation score	5

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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Cellular Component

External links

PDB	RCSB:3kx2, PDBe:3kx2, PDBj:3kx2
PDBsum	3kx2
PubMed	20168331
UniProt	P53131\|PRP43_YEAST Pre-mRNA-splicing factor ATP-dependent RNA helicase PRP43 (Gene Name=PRP43)

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