Structure of PDB 5nrl Chain A Binding Site BS03

Receptor Information
>5nrl Chain A (length=2216) Species: 4932 (Saccharomyces cerevisiae) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
YTPKAEMPPEHLRKIINTHSDDKKAFLGALKYLPHAILKLLENMPHPWEQ
AKEVKVLYHTSGAITFVNETPRVIEPVYTAQWSATWIAMRREKRDRTHFK
RMRFPPFDDDEPPLSYEQHIENIEPLDPINLPLDSQDDEYVKDWLYDSRP
LEEDSKKVNGTSYKKWSFDLPEMSNLYRLSTPLRDEVTDKNYYYLFDKKS
FFNGKALNNAIPGGPKFEPLYPREEEEDYNEFNSIDRVIFRVPIRSEYKV
AFPHLYNSRPRSVRIPWYNNPVSCIIQNDTPALFFDPSLNPIPHFDFTLP
EDFAPLLAEEEELILPNTKDAMSLYHSPFPFNRTKGKMVRAQDVALAKKW
FLQHPDEEYPVKVKVSYQKLLKNYVLNELHPTLPTNHNKTKLLKSLKNTK
YFQQTTIDWVEAGLQLCRQGHNMLNLLIHRKGLTYLHLDYNFNLKPTKTL
TTKERKKSRLGNSFHLMRELLKMMKLIVDTHVQFRLGNVDAFQLADGIHY
ILNHIGQLTGIYRYKYKVMHQIRACKDLKHIIYYKFNKNLGKGPGCGFWQ
PAWRVWLNFLRGTIPLLERYIGNLITRQFEDAYYDLELRNSVMDDILEMM
PESIRQKKARTILQHLSEAWRCWKANIPWDVPGMPAPIKKIIERYIKSKA
DAWVSAAHYNRERIKRGAHVEKTMVKKNLGRLTRLWIKNEQERQRQIQKN
GPEITPEEATTIFSVMVEWLESRSFSPIPFPPLTYKNDTKILVLALEDLK
DVYASKVRLNASEREELALIEEAYDNPHDTLNRIKKYLLTQRVFKPVDIT
MMENYQNISPVYSVDPLEKITDAYLDQYLWYEADQRKLFPNWIKPSDSEI
PPLLVYKWTQGINNLSEIWDVSRGQSAVLLETTLGEMAEKIDFTLLNRLL
RLIVDPNIADYITAKNNVVINFKDMSHVNKYGLIRGLKFASFIFQYYGLV
IDLLLLGQERATDLAGPANNPNEFMQFKSKEVEKAHPIRLYTRYLDRIYM
LFHFEEDEGEELTDEYLAENPDPNFENSIGYNNRKCWPKDSRMRLIRQDV
NLGRAVFWEIQSRVPTSLTSIKWENAFVSVYSKNNPNLLFSMCGFEVRIL
PRQRMEEVVSNDEGVWDLVDERTKQRTAKAYLKVSEEEIKKFDSRIRGIL
MASGSTTFTKVAAKWNTSLISLFTYFREAIVATEPLLDILVKGETRIQNR
VKLGLNSKMPTRFPPAVFYTPKELGGLGMISASHILIPASDLSWSKQTDT
GITHFRAGMTHEDEKLIPTIFRYITTWENEFLDSQRVWAEYATKRQEAIQ
QNRRLAFEELEGSWDRGIPRISTLFQRDRHTLAYDRGHRIRREFKQYSLE
RNSPFWWTNSHHDGKLWNLNAYRTDVIQALGGIETILEHTLFKGTGFNSW
EGLFWEKASGFEDSMQFKKLTHAQRTGLSQIPNRRFTLWWSPTINRANVY
VGFLVQLDLTGIFLHGKIPTLKISLIQIFRAHLWQKIHESIVFDICQILD
GELDVLQIESVTKETVHPRKSYKMNSSAADITMESVHEWEVSKPSLLHET
NDSFKGLITNKMWFDVQLRYGDYDSHDISRYVRAKFLDYTTDNVSMYPSP
TGVMIGIDLAYNMYDAYGNWFNGLKPLIQNSMRTIMKANPALYVLRERIR
KGLQIYQSSVQEPFLNSSNYAELFNNDIKLFVDDTNVYRVTVHKNVATKA
INGCIFTLNPKTGHLFLKIIHTSVWAGQKRLSQLAKWKTAEEVSALVRSL
PKEEQPKQIIVTRKAMLDPLEVHMLDFPNIAIRPTELRLPFSAAMSIDKL
SDVVMKATEPQMVLFNIYDDWLDRISSYTAFSRLTLLLRALKTNEESAKM
ILLSDPTITIKSYHLWPSFTDEQWITIESQMRDLILTEYGRKYNVNISAL
TQTEIKDIILGQNIKAPSVKRQKMAELEAARSEKQMKTKTINAQGEEIVV
VASADYESQTFSSKNEWRKSAIANTLLYLRLKNIYVSADDFVEEQNVYVL
PKNLLKKFIEISDVKIQVAAFIYGMSAKDHPKVKEIKTVVLVPQLGHVGS
VQISNIPDIGDLPDTEGLELLGWIHTQTEELKFMAASEVATHSKLFADKK
RDCIDISIFSTPGSVSLSAYNLTDEGYQWGEENKDIMNVLSEGFEPTFST
HAQLLLSDRITGNFIIPSGNVWNYTFMGTAFNQEGDYNFKYGIPLEFYNE
MHRPVHFLQFSELAGD
Ligand information
>5nrl Chain 6 (length=95) [Search RNA sequence] [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
guucgcgaacuucguggacauuuggucaauuugaaacaauacagagauca
gcaguuccccugcauaaggaugaaccguucaaagagauuuguuuu
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]
PDB5nrl Structure of a pre-catalytic spliceosome.
Resolution7.2 Å
Binding residue
(original residue number in PDB)		P515 V516 T607 K611 R614 H659 Q662 Y671 K681 K684 K697 S1377 K1378 F1623 D1628 L1629 G1636 K1637 K1642 I1646 Q1647 R1650 A1651 H1652 R1689
Binding residue
(residue number reindexed from 1)		P360 V361 T452 K456 R459 H504 Q507 Y516 K526 K529 K542 S1207 K1208 F1453 D1458 L1459 G1466 K1467 K1472 I1476 Q1477 R1480 A1481 H1482 R1519
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:5nrl, PDBe:5nrl, PDBj:5nrl
PDBsum5nrl
PubMed28530653
UniProtP33334|PRP8_YEAST Pre-mRNA-splicing factor 8 (Gene Name=PRP8)

[Back to BioLiP]