Structure of PDB 6bk8 Chain A

Receptor sequence

>6bk8A (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

3D structure

• PDB: 6bk8 Structure of the yeast spliceosomal postcatalytic P complex.
• Chain: A
• Resolution: 3.3 Å

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	rna	A	D751 D755 R759 Q784 S787 W790 K794 K847 R851 R854 N930 R934 K1093 D1094	D605 D609 R613 Q638 S641 W644 K648 K701 R705 R708 N784 R788 K947 D948
BS02	rna	A	N126 Y128 E204 T205 R207 R284 G295 T296 S297 K334 K340 E353 W402 F484 R495 D498 K503 K527 N532 E533 H535 T537 P539 N541 H542 K544 K546 K549 K670 Y671 K672 H675 R709 N713 R716 G717 H839 E841 L1373 K1378	N1 Y3 E79 T80 R82 R159 G170 T171 S172 K209 K215 E228 W272 F338 R349 D352 K357 K381 N386 E387 H389 T391 P393 N395 H396 K398 K400 K403 K524 Y525 K526 H529 R563 N567 R570 G571 H693 E695 L1227 K1232
BS03	rna	A	S151 K152 M153 K608 E609 K611 R614 G616 S618 Y725 N728 R732 R737 K743 T744 Q748 R749 Y753 T1591 H1592 H1863 E1867 N1869 A1900 K1903	S26 K27 M28 K462 E463 K465 R468 G470 S472 Y579 N582 R586 R591 K597 T598 Q602 R603 Y607 T1445 H1446 H1717 E1721 N1723 A1754 K1757
BS04	rna	A	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	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
BS05	rna	A	T607 K611 G1580 F1581 A1593 Q1594 G1597 I1601 R1604 Q1647 Y1826 F1834 Y1858 N1869 V1870 T1872 K1903 R1904 Q1907 R1937 E1960 Y2067 P2091 R2095	T461 K465 G1434 F1435 A1447 Q1448 G1451 I1455 R1458 Q1501 Y1680 F1688 Y1712 N1723 V1724 T1726 K1757 R1758 Q1761 R1791 E1814 Y1921 P1945 R1949
BS06	IHP	A	R236 K517 H659 K684 H685 Y688 Y689 K697	R111 K371 H513 K538 H539 Y542 Y543 K551

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)