Structure of PDB 7w59 Chain A

Receptor sequence
>7w59A (length=1984) Species: 9606 (Homo sapiens) [Search protein sequence]
MSEEKLQEKARKWQQLQAKRYAEKRKFGFVDAQKEDMPPEHVRKIIRDHG
DMTNRKFRHDKRVYLGALKYMPHAVLKLLENMPMPWEQIRDVPVLYHITG
AISFVNEIPWVIEPVYISQWGSMWIMMRREKRDRRHFKRMRFPPFDDEEP
PLDYADNILDVEPLEAIQLELDPEEDAPVLDWFYDHQPLRDSRKYVNGST
YQRWQFTLPMMSTLYRLANQLLTDLVDDNYFYLFDLKAFFTSKALNMAIP
GGPKFEPLVRDWNEFNDINKIIIRQPIRTEYKIAFPYLYNNLPHHVHLTW
YHTPNVVFIKTEDPDLPAFYFDPLINPISHRHSVKSQEPLPDDDEEFELP
EFVEPFLKDTPLYTDNTANGIALLWAPRPFNLRSGRTRRALDIPLVKNWY
REHCPAGQPVKVRVSYQKLLKYYVLNALKHRPPKAQKKRYLFRSFKATKF
FQSTKLDWVEVGLQVCRQGYNMLNLLIHRKNLNYLHLDYNFNLKPVKTLT
TKERKKSRFGNAFHLCREVLRLTKLVVDSHVQYRLGNVDAFQLADGLQYI
FAHVGQLTGMYRYKYKLMRQIRMCKDLKHLIYYRFNTGPVGKGPGCGFWA
AGWRVWLFFMRGITPLLERWLGNLLARQFEGRHSKGVAKTVTKQRVESHF
DLELRAAVMHDILDMMPEGIKQNKARTILQHLSEAWRCWKANIPWKVPGL
PTPIENMILRYVKAKADWWTNTAHYNRERIRRGATVDKTVCKKNLGRLTR
LYLKAEQERQHNYLKDGPYITAEEAVAVYTTTVHWLESRRFSPIPFPPLS
YKHDTKLLILALERLKEAYSVKSRLNQSQREELGLIEQAYDNPHEALSRI
KRHLLTQRAFKEVGIEFMDLYSHLVPVYDVEPLEKITDAYLDQYLWYEAD
KRRLFPPWIKPADTEPPPLLVYKWCQGINNLQDVWETSEGECNVMLESRF
EKMYEKIDLTLLNRLLRLIVDHNIADYMTAKNNVVINYKDMNHTNSYGII
RGLQFASFIVQYYGLVMDLLVLGLHRASEMAGPPQMPNDFLSFQDIATEA
AHPIRLFCRYIDRIHIFFRFTADEARDLIQRYLTEHPDPNNENIVGYNNK
KCWPRDARMRLMKHDVNLGRAVFWDIKNRLPRSVTTVQWENSFVSVYSKD
NPNLLFNMCGFECRILPKCRTSYEEFTHKDGVWNLQNEVTKERTAQCFLR
VDDESMQRFHNRVRQILMASGSTTFTKIVNKWNTALIGLMTYFREAVVNT
QELLDLLVKCENKIQTRIKIGLNSKMPSRFPPVVFYTPKELGGLGMLSMG
HVLIPQSDLRWSKQTDVGITHFRSGMSHEEDQLIPNLYRYIQPWESEFID
SQRVWAEYALKRQEAIAQNRRLTLEDLEDSWDRGIPRINTLFQKDRHTLA
YDKGWRVRTDFKQYQVLKQNPFWWTHQRHDGKLWNLNNYRTDMIQALGGV
EGILEHTLFKGTYFPTWEGLFWEKASGFEESMKWKKLTNAQRSGLNQIPN
RRFTLWWSPTINRANVYVGFQVQLDLTGIFMHGKIPTLKISLIQIFRAHL
WQKIHESIVMDLCQVFDQELDALEIETVQKETIHPRKSYKMNSSCADILL
FASYKWNVSRPSLLADSKDVMDSTTTQKYWIDIQLRWGDYDSHDIERYAR
AKFLDYTTDNMSIYPSPTGVLIAIDLAYNLHSAYGNWFPGSKPLIQQAMA
KIMKANPALYVLRERIRKGLQLYSSEPTEPYLSSQNYGELFSNQIIWFVD
DTNVYRVTIHKTFEGNLTTKPINGAIFIFNPRTGQLFLKIIHTSVWAGQK
RLGQLAKWKTAEEVAALIRSLPVEEQPKQIIVTRKGMLDPLEVHLLDFPN
IVIKGSELQLPFQACLKVEKFGDLILKATEPQMVLFNLYDDWLKTISSYT
AFSRLILILRALHVNNDRAKVILKPDKTTITEPHHIWPTLTDEEWIKVEV
QLKDLILADYGKKNNVNVASLTQSEIRDIILGME
3D structure
PDB7w59 Mechanism of exon ligation by human spliceosome.
ChainA
Resolution3.6 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 rna A P274 K278 R309 C435 V441 Q448 R539 Y592 R593 Y596 R603 S1305 K1306 M1307 P1308 Y1548 P250 K254 R278 C404 V410 Q417 R508 Y561 R562 Y565 R572 S1274 K1275 M1276 P1277 Y1517
BS02 rna A R82 H83 T532 K533 K536 V852 S854 R855 G1252 S1253 K1258 L1467 N1468 K1505 E1510 T1519 N1520 A1521 Q1522 R1523 L1526 N1797 L1798 T1800 R1865 R58 H59 T501 K502 K505 V821 S823 R824 G1221 S1222 K1227 L1436 N1437 K1474 E1479 T1488 N1489 A1490 Q1491 R1492 L1495 N1766 L1767 T1769 R1834
BS03 rna A G52 F53 V54 Q57 K101 I132 W134 N221 S223 T224 K267 E280 R284 R409 R417 R419 R420 D423 P425 K428 K452 K460 H461 P464 Q467 K469 R474 K595 Y596 K597 R600 R635 F639 R642 G643 P646 T766 D768 K1306 G28 F29 V30 Q33 K77 I108 W110 N197 S199 T200 K243 E256 R260 R378 R386 R388 R389 D392 P394 K397 K421 K429 H430 P433 Q436 K438 R443 K564 Y565 K566 R569 R604 F608 R611 G612 P615 T735 D737 K1275
BS04 rna A Q39 K511 N512 E534 K536 K537 R539 G541 A543 W651 N654 R658 R663 T671 Q675 R676 S679 L683 T1793 T1799 K1801 A1828 G1829 Q15 K480 N481 E503 K505 K506 R508 G510 A512 W620 N623 R627 R632 T640 Q644 R645 S648 L652 T1762 T1768 K1770 A1797 G1798
BS05 rna A D682 R686 N704 K705 R707 Q711 S714 K746 K773 K774 R778 R781 S854 R855 L856 R861 K1020 D1021 W1515 K1516 D651 R655 N673 K674 R676 Q680 S683 K715 K742 K743 R747 R750 S823 R824 L825 R830 K989 D990 W1484 K1485
BS06 IHP A R163 K442 H584 K609 H610 Y613 K623 R139 K411 H553 K578 H579 Y582 K592
Gene Ontology
Molecular Function
GO:0003723 RNA 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:0070530 K63-linked polyubiquitin modification-dependent protein binding
GO:0097157 pre-mRNA intronic binding
GO:0140492 metal-dependent deubiquitinase activity
Biological Process
GO:0000244 spliceosomal tri-snRNP complex assembly
GO:0000375 RNA splicing, via transesterification reactions
GO:0000398 mRNA splicing, via spliceosome
GO:0006397 mRNA processing
GO:0008380 RNA splicing
GO:0071222 cellular response to lipopolysaccharide
GO:0071356 cellular response to tumor necrosis factor
Cellular Component
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005681 spliceosomal complex
GO:0005682 U5 snRNP
GO:0016020 membrane
GO:0016607 nuclear speck
GO:0030532 small nuclear ribonucleoprotein complex
GO:0046540 U4/U6 x U5 tri-snRNP complex
GO:0071005 U2-type precatalytic spliceosome
GO:0071006 U2-type catalytic step 1 spliceosome
GO:0071007 U2-type catalytic step 2 spliceosome
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:7w59, PDBe:7w59, PDBj:7w59
PDBsum7w59
PubMed35705093
UniProtQ6P2Q9|PRP8_HUMAN Pre-mRNA-processing-splicing factor 8 (Gene Name=PRPF8)

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