Structure of PDB 5gmk Chain A Binding Site BS01

Receptor Information
>5gmk Chain A (length=1910) 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
SLNPIGDFTLPEDFAPLLAEEEELILPNTKDAMSLYHSPFPFNRTKGKMV
RAQDVALAKKWFLQHPDEEYPVKVKVSYQKLLKNYVLNELHPTLPTNHNK
TKLLKSLKNTKYFQQTTIDWVEAGLQLCRQGHNMLNLLIHRKGLTYLHLD
YNFNLKPTKTLTTKERKKSRLGNSFHLMRELLKMMKLIVDTHVQFRLGNV
DAFQLADGIHYILNHIGQLTGIYRYKYKVMHQIRACKDLKHIIYYKFNKN
LGKGPGCGFWQPAWRVWLNFLRGTIPLLERYIGNLITRQFEGRSNEIVKT
TTKQRLDAYYDLELRNSVMDDILEMMPESIRQKKARTILQHLSEAWRCWK
ANIPWDVPGMPAPIKKIIERYIKSKADAWVSAAHYNRERIKRGAHVEKTM
VKKNLGRLTRLWIKNEQERQRQIQKNGPEITPEEATTIFSVMVEWLESRS
FSPIPFPPLTYKNDTKILVLALEDLKDVYASKVRLNASEREELALIEEAY
DNPHDTLNRIKKYLLTQRVFKPVDITMMENYQNISPVYSVDPLEKITDAY
LDQYLWYEADQRKLFPNWIKPSDSEIPPLLVYKWTQGINNLSEIWDVSRG
QSAVLLETTLGEMAEKIDFTLLNRLLRLIVDPNIADYITAKNNVVINFKD
MSHVNKYGLIRGLKFASFIFQYYGLVIDLLLLGQERATDLAGPANNPNEF
MQFKSKEVEKAHPIRLYTRYLDRIYMLFHFEEDEGEELTDEYLAENPDPN
FENSIGYNNRKCWPKDSRMRLIRQDVNLGRAVFWEIQSRVPTSLTSIKWE
NAFVSVYSKNNPNLLFSMCGFEVRILPRQRMEEVVSNDEGVWDLVDERTK
QRTAKAYLKVSEEEIKKFDSRIRGILMASGSTTFTKVAAKWNTSLISLFT
YFREAIVATEPLLDILVKGETRIQNRVKLGLNSKMPTRFPPAVFYTPKEL
GGLGMISASHILIPASDLSWSKQTDTGITHFRAGMTHEDEKLIPTIFRYI
TTWENEFLDSQRVWAEYATKRQEAIQQNRRLAFEELEGSWDRGIPRISTL
FQRDRHTLAYDRGHRIRREFKQYSLERNSPFWWTNSHHDGKLWNLNAYRT
DVIQALGGIETILEHTLFKGTGFNSWEGLFWEKSQIPNRRFTLWWSPTIN
RANVYVGFLVQLDLTGIFLHGKIPTLKISLIQIFRAHLWQKIHESIVFDI
CQILDGELDVLQIESVTKETVHPRKSYKMNSSAADITMESVHEWEVSKPS
LLHETNDSFKGLITNKMWFDVQLRYGDYDSHDISRYVRAKFLDYTTDNVS
MYPSPTGVMIGIDLAYNMYDAYGNWFNGLKPLIQNSMRTIMKANPALYVL
RERIRKGLQIYQSSYAELFNNDIKLFVDDTNVYRVTVHKTFEGNVATKAI
NGCIFTLNPKTGHLFLKIIHTSVWAGQKRLSQLAKWKTAEEVSALVRSLP
KEEQPKQIIVTRKAMLDPLEVHMLDFPNIAIRPTELRLPFSAAMSIDKLS
DVVMKATEPQMVLFNIYDDWLDRISSYTAFSRLTLLLRALKTNEESAKMI
LLSDPTITIKSYHLWPSFTDEQWITIESQMRDLILTEYGRKYNVNISALT
QTEIKDIILG
Ligand information
>5gmk Chain D (length=117) [Search RNA sequence] [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
ggaggucaacaucaagaacugugggccuuugccuauagaacuuauaacga
acaugguucuugccuuuuaccagaaccauccggguguugucuccauccau
auuuuuuggaacuuuuc
<<<<<.<<<<<<<.....<<<<<<<<....>>>>>>>>............
..<<<<<<<<...........>>>>>>>>...>>>>>>>>>>>>......
.................
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB5gmk Structure of a yeast catalytic step I spliceosome at 3.4 angstrom resolution
Resolution3.4 Å
Binding residue
(original residue number in PDB)		Y128 K190 T205 R284 T296 S297 K333 K340 F352 E353 L355 W402 F484 R488 R495 D498 K503 N532 H535 L538 P539 N541 K546 K549 K670 Y671 K672 H675 R709 N713 R716 G717 P720 L721 H839 K842
Binding residue
(residue number reindexed from 1)		Y2 K64 T79 R158 T170 S171 K207 K214 F226 E227 L229 W276 F340 R344 R351 D354 K359 N388 H391 L394 P395 N397 K402 K405 K526 Y527 K528 H531 R565 N569 R572 G573 P576 L577 H695 K698
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

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:5gmk, PDBe:5gmk, PDBj:5gmk
PDBsum5gmk
PubMed27445308
UniProtP33334|PRP8_YEAST Pre-mRNA-splicing factor 8 (Gene Name=PRP8)

[Back to BioLiP]