Structure of PDB 5lj3 Chain A Binding Site BS01

Receptor Information
>5lj3 Chain A (length=1922) Species: 4932 (Saccharomyces cerevisiae) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
YTPKAEMPPEHLRKIINTHSDMASKMYNTDKKAFLGALKYLPHAILKLLE
NMPHPWEQAKEVKVLYHTSGAITFVNETPRVIEPVYTAQWSATWIAMRRE
KRDRTHFKRMRFPPFDDDEPPLSYEQHIENIEPLDPINLPLDSQDDEYVK
DWLYDSRPLEEDSKKVNGTSYKKWSFDLPEMSNLYRLSTPLRDEVTDKNY
YYLFDKKSFFNGKALNNAIPGGPKFEPLYPREEEEDYNEFNSIDRVIFRV
PIRSEYKVAFPHLYNSRPRSVRIPWYNNPVSCIIQNDEEYDTPALFFDPS
LEDFAPLLAEEEELILPNTKDAMSLYHSPFPFNRTKGKMVRAQDVALAKK
WFLQHPDEEYPVKVKVSYQKLLKNYVLNELHPTLPTNHNKTKLLKSLKNT
KYFQQTTIDWVEAGLQLCRQGHNMLNLLIHRKGLTYLHLDYNFNLKPTKT
LTTKERKKSRLGNSFHLMRELLKMMKLIVDTHVQFRLGNVDAFQLADGIH
YILNHIGQLTGIYRYKYKVMHQIRACKDLKHIIYYKFNKNLGKGPGCGFW
QPAWRVWLNFLRGTIPLLERYIGNLITRQFEGRSNEIVKTTTKQRLDAYY
DLELRNSVMDDILEMMPESIRQKKARTILQHLSEAWRCWKANIPWDVPGM
PAPIKKIIERYIKSKADAWVSAAHYNRERIKRGAHVEKTMVKKNLGRLTR
LWIKNEQERQRQIQKNGPEITPEEATTIFSVMVEWLESRSFSPIPFPPLT
YKNDTKILVLALEDLKDVYASKVRLNASEREELALIEEAYDNPHDTLNRI
KKYLLTQRVFKPVDITMMENYQNISPVYSVDPLEKITDAYLDQYLWYEAD
QRKLFPNWIKPSDSEIPPLLVYKWTQGINNLSEIWDVSRGQSAVLLETTL
GEMAEKIDFTLLNRLLRLIVDPNIADYITAKNNVVINFKDMSHVNKYGLI
RGLKFASFIFQYYGLVIDLLLLGQERATDLAGPANNPNEFMQFKSKEVEK
AHPIRLYTRYLDRIYMLFHFEEDEGEELTDEYLAENPDPNFENSIGYNNR
KCWPKDSRMRLIRQDVNLGRAVFWEIQSRVPTSLTSIKWENAFVSVYSKN
NPNLLFSMCGFEVRILPRQRMEEVVSNDEGVWDLVDERTKQRTAKAYLKV
SEEEIKKFDSRIRGILMASGSTTFTKVAAKWNTSLISLFTYFREAIVATE
PLLDILVKGETRIQNRVKLGLNSKMPTRFPPAVFYTPKELGGLGMISASH
ILIPASDLSWSKQTDTGITHFRAGMTHEDEKLIPTIFRYITTWENEFLDS
QRVWAEYATKRQEAIQQNRRLAFEELEGSWDRGIPRISTLFQRDRHTLAY
DRGHRIRREFKQYSLERNSPFWWTNSHHDGKLWNLNAYRTDVIQALGGIE
TILEHTLFKGTGFNSWEGLFWEKASGFEDSMQFKKLTHAQRTGLSQIPNR
RFTLWWSPTINRANVYVGFLVQLDLTGIFLHGKIPTLKISLIQIFRAHLW
QKIHESIVFDICQILDGELDVLQIESVTKETVHPRKSYKMNSSAADITME
SVHEWEVSKPSLLHETNDSFKGLITNKMWFDVQLRYGDYDSHDISRYVRA
KFLDYTTDNVSMYPSPTGVMIGIDLAYNMYDAYGNWFNGLKPLIQNSMRT
IMKANPALYVLRERIRKGLQIYQSSNYAELFNNDIKLFVDDTNVYRVTVH
KTFEGNVATKAINGCIFTLNPKTGHLFLKIIHTSVWAGQKRLSQLAKWKT
AEEVSALVRSLPKEEQPKQIIVTRKAMLDPLEVHMLDFPNIAIRPTELRL
PFSAAMSIDKLSDVVMKATEPQMVLFNIYDDWLDRISSYTAFSRLTLLLR
ALKTNEESAKMILLSDPTITIKSYHLWPSFTDEQWITIESQMRDLILTEY
GRKYNVNISALTQTEIKDIILG
Ligand information
>5lj3 Chain U (length=141) [Search RNA sequence] [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
cagcuuuacagaucaauggcggagggaggucaacaucaagaacugugggc
gccuauagaacuuauaacgaacaugguucuugccuuuuaccagaaccauc
cggguguugucuccauagaaacagguaaagcuguauuuuuu
<<<<<<<<<.......<.......<<<<<.<<<<<<<.....<<<<<<<.
.>>>>>>>..............<<<<<<<<...........>>>>>>>>.
..>>>>>>>>>>>>......>...>>>>>>>>>........
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB5lj3 Cryo-EM structure of the spliceosome immediately after branching.
Resolution3.8 Å
Binding residue
(original residue number in PDB)		Y128 T129 P130 H170 E204 T205 R207 R284 G295 T296 S297 K300 K325 K334 K340 F352 E353 W402 F484 R488 K492 R495 D498 K503 K527 N532 H535 T537 L538 P539 N541 K544 K549 K670 Y671 K672 H675 Q676 R709 N713 F714 R716 G717 P720 H839 V840 E841 K842 N1369 R1370
Binding residue
(residue number reindexed from 1)		Y1 T2 P3 H43 E77 T78 R80 R157 G168 T169 S170 K173 K198 K207 K213 F225 E226 W275 F330 R334 K338 R341 D344 K349 K373 N378 H381 T383 L384 P385 N387 K390 K395 K516 Y517 K518 H521 Q522 R555 N559 F560 R562 G563 P566 H685 V686 E687 K688 N1215 R1216
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:5lj3, PDBe:5lj3, PDBj:5lj3
PDBsum5lj3
PubMed27459055
UniProtP33334|PRP8_YEAST Pre-mRNA-splicing factor 8 (Gene Name=PRP8)

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