Structure of PDB 6zym Chain A

Receptor sequence

>6zymA (length=1722) Species: 9606 (Homo sapiens)

SEEKLQEKARKWQQLQAKRYAEKRKFGFVDAQKEDMPPEHVRKIIRDHGD
MTNRKFRHDKRVYLGALKYMPHAVLKLLENMPMPWEQIRDVPVLYHITGA
ISFVNEIPWVIEPVYISQWGSMWIMMRREKRDRRHFKRMRFPPFDDEEPP
LDYADNILDVEPLEAIQLELDPEEDAPVLDWFYDHQPLRDSRKYVNGSTY
QRWQFTLPMMSTLYRLANQLLTDLVDDNYFYLFDLKAFFTSKALNMAIPG
GPKFEPLVRDINLQDEDWNEFNDINKIIIRQPIRTEYKIAFPYLYNNLPH
HVHLTWYHTPNVVFIKTEDPDLPAFYFDPLINPISHRHSVKSQEPLPDDD
EEFELPEFVEPFLKDTPLYTDNTANGIALLWAPRPFNLRSGRTRRALDIP
LVKNWYREHCPAGQPVKVRVSYQKLLKYYVLNALKHRPPKAQKKRYLFRS
FKATKFFQSTKLDWVEVGLQVCRQGYNMLNLLIHRKNLNYLHLDYNFNLK
PVKTLTTKERKKSRFGNAFHLCREVLRLTKLVVDSHVQYRLGNVDAFQLA
DGLQYIFAHVGQLTGMYRYKYKLMRQIRMCKDLKHLIYYRFNTGPVGKGP
GCGFWAAGWRVWLFFMRGITPLLERWLGNLLARQFEGRHSKGVAKTVTKQ
RVESHFDLELRAAVMHDILDMMPEGIKQNKARTILQHLSEAWRCWKANIP
WKVPGLPTPIENMILRYVKAKADWWTNTAHYNRERIRRGATVDKTVCKKN
LGRLTRLYLKAEQERQHNYLKDGPYITAEEAVAVYTTTVHWLESRRFSPI
PFPPLSYKHDTKLLILALERLKEAYSVKSRLNQSQREELGLIEQAYDNPH
EALSRIKRHLLTQRAFKEVGIEFMDLYSHLVPVYDVEPLEKITDAYLDQY
LWYEADKRRLFPPWIKPADTEPPPLLVYKWCQGINNLQDVWETSEGECNV
MLESRFEKMYEKIDLTLLNRLLRLIVDHNIADYMTAKNNVVINYKDMNHT
NSYGIIRGLQFASFIVQYYGLVMDLLVLGLHRASEMAGPPQMPNDFLSFQ
DIATEAAHPIRLFCRYIDRIHIFFRFTADEARDLIQRYLTEHPDPNNENI
VGYNNKKCWPRDARMRLMKHDVNLGRAVFWDIKNRLPRSVTTVQWENSFV
SVYSKDNPNLLFNMCGFECRILPKCRTSYEEFTHKDGVWNLQNEVTKERT
AQCFLRVDDESMQRFHNRVRQILMASGSTTFTKIVNKWNTALIGLMTYFR
EAVVNTQELLDLLVKCENKIQTRIKIGLNSKMPSRFPPVVFYTPKELGGL
GMLSMGHVLIPQSDLRWSKQTDVGITHFRSGMSHEEDQLIPNLYRYIQPW
ESEFIDSQRVWAEYALKRQEAIAQNRRLTLEDLEDSWDRGIPRINTLFQK
DRHTLAYDKGWRVRTDFKQYQVLKQNPFWWTHQRHDGKLWNLNNYRTDMI
QALGGVEGILEHTLFKGTYFPTWEGLFWEKASGFEESMKRSGLNQIPNRR
FTLWWSPTINRANVYVGFQVQLDLTGIFMHGKIPTLKISLIQIFRAHLWQ
KIHESIVMDLCQVFDQELDALEIETVQKETIHPRKSYKMNSSCADILLFA
SYKWNVSRPSLLADSKDVMDSTTTQKYWIDIQLRWGDYDSHDIERYARAK
FLDYTTDNMSIYPSPTGVLIAIDLAYNLHSAYGNWFPGSKPLIQQAMAKI
MKANPALYVLRERIRKGLQLYS

3D structure

• PDB: 6zym Structural Insights into the Roles of Metazoan-Specific Splicing Factors in the Human Step 1 Spliceosome.
• Chain: A
• Resolution: 3.4 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	T529 E678 D682 R707 S714 W717 K746 K774 G777 R778 R781 R855 N857 Q858 R861 K1020 D1021 S1253 T1255 N1531 P1567 T1568 Q1575	T504 E653 D657 R682 S689 W692 K721 K749 G752 R753 R756 R830 N832 Q833 R836 K995 D996 S1228 T1230 N1498 P1534 T1535 Q1542
BS02	rna	A	F53 H97 K101 I132 W134 G222 S223 T224 K267 E280 R409 R419 R420 D423 K428 L456 N457 K460 H461 P463 P464 K465 A466 K469 R474 K595 Y596 K597 R600 Q601 R635 F639 R642 G643 P646 L647 V767 D768 K769 R1298 K1306	F28 H72 K76 I107 W109 G197 S198 T199 K242 E255 R384 R394 R395 D398 K403 L431 N432 K435 H436 P438 P439 K440 A441 K444 R449 K570 Y571 K572 R575 Q576 R610 F614 R617 G618 P621 L622 V742 D743 K744 R1273 K1281
BS03	rna	A	R35 K511 N512 T531 E534 K536 K537 R539 G541 A543 W651 N654 R658 R663 T671 T673 Q675 R676 S679 L683	R10 K486 N487 T506 E509 K511 K512 R514 G516 A518 W626 N629 R633 R638 T646 T648 Q650 R651 S654 L658
BS04	rna	A	R79 R82 N512 K533 K1258 L1448 K1449 L1526 R1578 K1749	R54 R57 N487 K508 K1233 L1423 K1424 L1493 R1545 K1716
BS05	rna	A	K278 V441 R444 V445 Q448 Y592 R593 Y596 K1306 M1307 P1308 Y1548 K1565	K253 V416 R419 V420 Q423 Y567 R568 Y571 K1281 M1282 P1283 Y1515 K1532
BS06	peptide	A	V527 K528 T531	V502 K503 T506
BS07	IHP	A	K442 H584 K609 H610 Y613 Y614 K623 G624	K417 H559 K584 H585 Y588 Y589 K598 G599

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0017070 U6 snRNA binding
• GO:0030623 U5 snRNA binding

Biological Process

• GO:0000398 mRNA splicing, via spliceosome

Cellular Component

• GO:0005681 spliceosomal complex

External links

• PDB: RCSB:6zym, PDBe:6zym, PDBj:6zym
• PDBsum: 6zym
• PubMed: 33007253
• UniProt: Q6P2Q9|PRP8_HUMAN Pre-mRNA-processing-splicing factor 8 (Gene Name=PRPF8)