Structure of PDB 6j6q Chain A

Receptor sequence
>6j6qA (length=1913) Species: 559292 (Saccharomyces cerevisiae S288C) [Search protein sequence]
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
3D structure
PDB6j6q Structures of the Catalytically Activated Yeast Spliceosome Reveal the Mechanism of Branching.
ChainA
Resolution3.7 Å
3D
structure
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Enzymatic activity
Enzyme Commision number ?
Interaction with ligand
Site
#		 Ligand Ligand
chain		 Binding residues on receptor
(original residue number in PDB)		 Binding residues on receptor
(residue number reindexed from 1)		 Binding affinity
BS01 peptide A N343 A345 E353 P354 R380 S381 K1362 L1406 D1411 I1422 T1423 H1424 F1425 R1426 A1427 T1430 N217 A219 E227 P228 R254 S255 K1221 L1265 D1270 I1281 T1282 H1283 F1284 R1285 A1286 T1289
BS02 rna A P347 Q523 T607 K608 R610 K611 R614 Y667 R668 Y671 M674 R678 S925 K926 R928 M972 S1325 K1330 S1377 K1378 M1379 P1380 R1521 K1535 Q1600 Y1620 K1637 R1650 E1817 R1904 S1906 P221 Q382 T466 K467 R469 K470 R473 Y526 R527 Y530 M533 R537 S784 K785 R787 M831 S1184 K1189 S1236 K1237 M1238 P1239 R1380 K1394 Q1438 Y1458 K1475 R1488 E1655 R1732 S1734
BS03 rna A Y128 K190 E204 T205 R207 R284 G295 T296 S297 K299 K340 F352 E353 R358 W402 F484 R488 K492 R495 D498 K503 H535 P539 N541 K544 K546 K549 K552 K670 Y671 K672 H675 R709 N713 R716 G717 P720 K747 H839 E841 K842 R1370 L1373 Y2 K64 E78 T79 R81 R158 G169 T170 S171 K173 K214 F226 E227 R232 W276 F343 R347 K351 R354 D357 K362 H394 P398 N400 K403 K405 K408 K411 K529 Y530 K531 H534 R568 N572 R575 G576 P579 K606 H698 E700 K701 R1229 L1232
BS04 rna A S151 K152 M153 K555 K586 T606 E609 K611 K612 R614 G616 S618 Y725 N728 R732 R737 I741 K743 T744 T746 Q748 R749 A752 Y753 S25 K26 M27 K414 K445 T465 E468 K470 K471 R473 G475 S477 Y584 N587 R591 R596 I600 K602 T603 T605 Q607 R608 A611 Y612
BS05 rna A D755 R780 Q784 S787 W790 K794 K847 R851 R854 R928 L929 N930 A931 R934 K1093 D1094 S1325 T1327 P1602 N1603 T1640 I1643 E1867 G1868 N1869 V1870 D614 R639 Q643 S646 W649 K653 K706 R710 R713 R787 L788 N789 A790 R793 K952 D953 S1184 T1186 P1440 N1441 T1478 I1481 E1695 G1696 N1697 V1698
BS06 IHP A K517 H659 Y688 Y689 K697 G698 K376 H518 Y547 Y548 K556 G557
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:6j6q, PDBe:6j6q, PDBj:6j6q
PDBsum6j6q
PubMed30879786
UniProtP33334|PRP8_YEAST Pre-mRNA-splicing factor 8 (Gene Name=PRP8)

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