Structure of PDB 6bk8 Chain A Binding Site BS04

Receptor Information

>6bk8 Chain A (length=1960) Species: 559292 (Saccharomyces cerevisiae S288C)

NLYTPKAEMPPEHLRKIINTHSDMASKMYNTDKKAFLGALKYLPHAILKL
LENMPHPWEQAKEVKVLYHTSGAITFVNETPRVIEPVYTAQWSATWIAMR
REKRDRTHFKRMRFPPFDDDEPPLSYEQHIENIEPLDPINLPLDSQDDEY
VKDWLYDSRPLEEDSKKVNGTSYKKWSFDLPEMSNLYRLSTPLRDEVTDK
NYYYLFDKKSFFNGKALNNAIPGGPKFEPLYPRENEFNSIDRVIFRVPIR
SEYKVAFPHLYNSRPRSVRIPWYNNPVSCIIQNDEEYDTPALFFDPSLNP
IPHGDFTLPEDFAPLLAEEEELILPNTKDAMSLYHSPFPFNRTKGKMVRA
QDVALAKKWFLQHPDEEYPVKVKVSYQKLLKNYVLNELHPTLPTNHNKTK
LLKSLKNTKYFQQTTIDWVEAGLQLCRQGHNMLNLLIHRKGLTYLHLDYN
FNLKPTKTLTTKERKKSRLGNSFHLMRELLKMMKLIVDTHVQFRLGNVDA
FQLADGIHYILNHIGQLTGIYRYKYKVMHQIRACKDLKHIIYYKFNKNLG
KGPGCGFWQPAWRVWLNFLRGTIPLLERYIGNLITRQFEGRSNEIVKTTT
KQRLDAYYDLELRNSVMDDILEMMPESIRQKKARTILQHLSEAWRCWKAN
IPWDVPGMPAPIKKIIERYIKSKADAWVSAAHYNRERIKRGAHVEKTMVK
KNLGRLTRLWIKNEQERQRQIQKNGPEITPEEATTIFSVMVEWLESRSFS
PIPFPPLTYKNDTKILVLALEDLKDVYASKVRLNASEREELALIEEAYDN
PHDTLNRIKKYLLTQRVFKPVDITMMENYQNISPVYSVDPLEKITDAYLD
QYLWYEADQRKLFPNWIKPSDSEIPPLLVYKWTQGINNLSEIWDVSRGQS
AVLLETTLGEMAEKIDFTLLNRLLRLIVDPNIADYITAKNNVVINFKDMS
HVNKYGLIRGLKFASFIFQYYGLVIDLLLLGQERATDLAGPANNPNEFMQ
FKSKEVEKAHPIRLYTRYLDRIYMLFHFEEDEGEELTDEYLAENPDPNFE
NSIGYNNRKCWPKDSRMRLIRQDVNLGRAVFWEIQSRVPTSLTSIKWENA
FVSVYSKNNPNLLFSMCGFEVRILPRQRMEEVVSNDEGVWDLVDERTKQR
TAKAYLKVSEEEIKKFDSRIRGILMASGSTTFTKVAAKWNTSLISLFTYF
REAIVATEPLLDILVKGETRIQNRVKLGLNSKMPTRFPPAVFYTPKELGG
LGMISASHILIPASDLSWSKQTDTGITHFRAGMTHEDEKLIPTIFRYITT
WENEFLDSQRVWAEYATKRQEAIQQNRRLAFEELEGSWDRGIPRISTLFQ
RDRHTLAYDRGHRIRREFKQYSLERNSPFWWTNSHHDGKLWNLNAYRTDV
IQALGGIETILEHTLFKGTGFNSWEGLFWEKASGFEDSMQFKKLTHAQRT
GLSQIPNRRFTLWWSPTINRANVYVGFLVQLDLTGIFLHGKIPTLKISLI
QIFRAHLWQKIHESIVFDICQILDGELDVLQIESVTKETVHPRKSYKMNS
SAADITMESVHEWEVSKPSLLHETNDSFKGLITNKMWFDVQLRYGDYDSH
DISRYVRAKFLDYTTDNVSMYPSPTGVMIGIDLAYNMYDAYGNWFNGLKP
LIQNSMRTIMKANPALYVLRERIRKGLQIYQSSVQEPFLNSSNYAELFNN
DIKLFVDDTNVYRVTVHKTFEGNVATKAINGCIFTLNPKTGHLFLKIIHT
SVWAGQKRLSQLAKWKTAEEVSALVRSLPKEEQPKQIIVTRKAMLDPLEV
HMLDFPNIAIRPTELRLPFSAAMSIDKLSDVVMKATEPQMVLFNIYDDWL
DRISSYTAFSRLTLLLRALKTNEESAKMILLSDPTITIKSYHLWPSFTDE
QWITIESQMRDLILTEYGRKYNVNISALTQTEIKDIILGQNIKAPSVKRQ
KMAELEAARS

Ligand information

>6bk8 Chain e (length=34)

uuuaauaaaaaaaguauauuuuuuuuuuuuuuau

..................................

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6bk8 Structure of the yeast spliceosomal postcatalytic P complex.
• Resolution: 3.3 Å
• Binding residue (original residue number in PDB): V516 V520 Q523 R614 Y667 R668 Y671 R678 K842 K926 S1325 K1330 K1378 M1379 P1380 F1477 R1497 R1521 P1524 F1525 K1535 W1537 R1543 H1592 Y1620 K1637
• Binding residue (residue number reindexed from 1): V370 V374 Q377 R468 Y521 R522 Y525 R532 K696 K780 S1179 K1184 K1232 M1233 P1234 F1331 R1351 R1375 P1378 F1379 K1389 W1391 R1397 H1446 Y1474 K1491

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:6bk8, PDBe:6bk8, PDBj:6bk8
• PDBsum: 6bk8
• PubMed: 29146870
• UniProt: P33334|PRP8_YEAST Pre-mRNA-splicing factor 8 (Gene Name=PRP8)