Structure of PDB 5gmk Chain A Binding Site BS03

Receptor Information

>5gmk Chain A (length=1910) Species: 559292 (Saccharomyces cerevisiae S288C)

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 L (length=127)

acgaaucucuuugccuuuuggcuuagaucaaguguaguaucuguucuuug
uaacaacuaaugaccucagaggcucaauuuguuacaauacauuuuuuggc
accgcgacccucgcacuuguggagucg

................................................<<
<<<<<<.<...<.<<<<.>>>>.>..>.>>>>>>>>..............
..<<...<<...........>>...>>

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5gmk Structure of a yeast catalytic step I spliceosome at 3.4 angstrom resolution
• Resolution: 3.4 Å
• Binding residue (original residue number in PDB): D755 K777 R780 Q784 S787 K794 K846 K847 R851 R854 R928 R934 K1093 D1094 T1327 P1602 N1603 P1639 T1640 I1643 V1870
• Binding residue (residue number reindexed from 1): D611 K633 R636 Q640 S643 K650 K702 K703 R707 R710 R784 R790 K949 D950 T1183 P1437 N1438 P1474 T1475 I1478 V1695

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

External links

• PDB: RCSB:5gmk, PDBe:5gmk, PDBj:5gmk
• PDBsum: 5gmk
• PubMed: 27445308
• UniProt: P33334|PRP8_YEAST Pre-mRNA-splicing factor 8 (Gene Name=PRP8)