Structure of PDB 6j6g Chain A Binding Site BS03

Receptor Information
>6j6g Chain A (length=1913) Species: 559292 (Saccharomyces cerevisiae S288C) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
LYTPKAEMPPEHLRKIINTHSDMASKMYNTDKKAFLGALKYLPHAILKLL
ENMPHPWEQAKEVKVLYHTSGAITFVNETPRVIEPVYTAQWSATWIAMRR
EKRDRTHFKRMRFPPFDDDEPPLSYEQHIENIEPLDPINLPLDSQDDEYV
KDWLYDSRPLEEDSKKVNGTSYKKWSFDLPEMSNLYRLSTPLRDEVTDKN
YYYLFDKKSFFNGKALNNAIPGGPKFEPLYPREEEEDYNEFNSIDRVIFR
VPIRSEYKVAFPHLYNSRPRSVRIPWYNNPVSCIIQNDEEYDTPALFFDP
SLNPIPHFGDFTLPEDFAPLLAEEEELILPNTKDAMSLYHSPFPFNRTKG
KMVRAQDVALAKKWFLQHPDEEYPVKVKVSYQKLLKNYVLNELHPTLPTN
HNKTKLLKSLKNTKYFQQTTIDWVEAGLQLCRQGHNMLNLLIHRKGLTYL
HLDYNFNLKPTKTLTTKERKKSRLGNSFHLMRELLKMMKLIVDTHVQFRL
GNVDAFQLADGIHYILNHIGQLTGIYRYKYKVMHQIRACKDLKHIIYYKF
NKNLGKGPGCGFWQPAWRVWLNFLRGTIPLLERYIGNLITRQFEGRSNEI
VKTTTKQRLDAYYDLELRNSVMDDILEMMPESIRQKKARTILQHLSEAWR
CWKANIPWDVPGMPAPIKKIIERYIKSKADAWVSAAHYNRERIKRGAHVE
KTMVKKNLGRLTRLWIKNEQERQRQIQKNGPEITPEEATTIFSVMVEWLE
SRSFSPIPFPPLTYKNDTKILVLALEDLKDVYASKVRLNASEREELALIE
EAYDNPHDTLNRIKKYLLTQRVFKPVDITMMENYQNISPVYSVDPLEKIT
DAYLDQYLWYEADQRKLFPNWIKPSDSEIPPLLVYKWTQGINNLSEIWDV
SRGQSAVLLETTLGEMAEKIDFTLLNRLLRLIVDPNIADYITAKNNVVIN
FKDMSHVNKYGLIRGLKFASFIFQYYGLVIDLLLLGQERATDLAGPANNP
NEFMQFKSKEVEKAHPIRLYTRYLDRIYMLFHFEEDEGEELTDEYLAENP
DPNFENSIGYNNRKCWPKDSRMRLIRQDVNLGRAVFWEIQSRVPTSLTSI
KWENAFVSVYSKNNPNLLFSMCGFEVRILPRQRMEEVVSNDEGVWDLVDE
RTKQRTAKAYLKVSEEEIKKFDSRIRGILMASGSTTFTKVAAKWNTSLIS
LFTYFREAIVATEPLLDILVKGETRIQNRVKLGLNSKMPTRFPPAVFYTP
KELGGLGMISASHILIPASDLSWSKQTDTGITHFRAGMTHEDEKLIPTIF
RYITTWENEFLDSQRVWAEYATKRQEAIQQNRRLAFEELEGSWDRGIPRI
STLFQRDRHTLAYDRGHRIRREFKQYSLERNSPFWWTNSHHDGKLWNLNA
YRTDVIQALGGIETILEHTLFKGTGFNSWEGLFWEKSQIPNRRFTLWWSP
TINRANVYVGFLVQLDLTGIFLHGKIPTLKISLIQIFRAHLWQKIHESIV
FDICQILDGELDVLQIESVTKETVHPRKSYKMNSSAADITMESVHEWEVS
KPSLLHETNDSFKGLITNKMWFDVQLRYGDYDSHDISRYVRAKFLDYTTD
NVSMYPSPTGVMIGIDLAYNMYDAYGNWFNGLKPLIQNSMRTIMKANPAL
YVLRERIRKGLQIYQSSYAELFNNDIKLFVDDTNVYRVTVHKTFEGNVAT
KAINGCIFTLNPKTGHLFLKIIHTSVWAGQKRLSQLAKWKTAEEVSALVR
SLPKEEQPKQIIVTRKAMLDPLEVHMLDFPNIAIRPTELRLPFSAAMSID
KLSDVVMKATEPQMVLFNIYDDWLDRISSYTAFSRLTLLLRALKTNEESA
KMILLSDPTITIKSYHLWPSFTDEQWITIESQMRDLILTEYGRKYNVNIS
ALTQTEIKDIILG
Ligand information
>6j6g Chain D (length=179) [Search RNA sequence] [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
aagcagcuuuacagaucaauggcggagggaggucaacaucaagaacugug
ggccuuugccuauagaacuuauaacgaacaugguucuugccuuuuaccag
aaccauccggguguugucuccauagaaacagguaaagcuguccguuacug
ugggcuugccauauuuuuuggaacuuuuc
...<<<<<.<<<<<.......<<<<..<<<<<.<<<<<<<.....<<<<<
<<<....>>>>>>>>..............<<<<<<<<...........>>
>>>>>>...>>>>>>>>>>>>......<<<<......>>>>>>>>..>>>
>>>>>.>>.....................
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB6j6g Structures of the Catalytically Activated Yeast Spliceosome Reveal the Mechanism of Branching.
Resolution3.2 Å
Binding residue
(original residue number in PDB)		Y128 H170 K174 K190 E204 T205 R207 R284 G295 T296 S297 K299 K340 F352 E353 R358 W402 F484 K492 R495 D498 K503 N532 H535 T537 P539 N541 K544 K549 K552 K670 Y671 K672 H675 Q676 R709 N713 R716 G717 P720 H839 E841 K842 L1373
Binding residue
(residue number reindexed from 1)		Y2 H44 K48 K64 E78 T79 R81 R158 G169 T170 S171 K173 K214 F226 E227 R232 W276 F343 K351 R354 D357 K362 N391 H394 T396 P398 N400 K403 K408 K411 K529 Y530 K531 H534 Q535 R568 N572 R575 G576 P579 H698 E700 K701 L1232
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0000386 second spliceosomal transesterification activity
GO:0003723 RNA binding
GO:0003729 mRNA binding
GO:0005515 protein binding
GO:0008233 peptidase activity
GO:0008237 metallopeptidase activity
GO:0017070 U6 snRNA binding
GO:0030619 U1 snRNA binding
GO:0030620 U2 snRNA binding
GO:0030623 U5 snRNA binding
GO:0097157 pre-mRNA intronic binding
Biological Process
GO:0000244 spliceosomal tri-snRNP complex assembly
GO:0000350 generation of catalytic spliceosome for second transesterification step
GO:0000387 spliceosomal snRNP assembly
GO:0000389 mRNA 3'-splice site recognition
GO:0000395 mRNA 5'-splice site recognition
GO:0000398 mRNA splicing, via spliceosome
GO:0006397 mRNA processing
GO:0008380 RNA splicing
Cellular Component
GO:0005634 nucleus
GO:0005681 spliceosomal complex
GO:0005682 U5 snRNP
GO:0005737 cytoplasm
GO:0046540 U4/U6 x U5 tri-snRNP complex
GO:0071013 catalytic step 2 spliceosome

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:6j6g, PDBe:6j6g, PDBj:6j6g
PDBsum6j6g
PubMed30879786
UniProtP33334|PRP8_YEAST Pre-mRNA-splicing factor 8 (Gene Name=PRP8)

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