Structure of PDB 6ahd Chain D Binding Site BS01

Receptor Information

>6ahd Chain D (length=1699) Species: 9606 (Homo sapiens)

RCQLPDGSFRRQRKGYEEVHVPALKPKPFGSEEQLLPVEKLPKYAQAGFE
GFKTLNRIQSKLYRAALETDENLLLCAPTGAGKTNVALMCMLREIGKHIN
MDGTINVDDFKIIYIAPMRSLVQEMVGSFGKRLATYGITVAELTGDHQLC
KEEISATQIIVCTPEKWDIITRKGGERTYTQLVRLIILDEIHLLHDDRGP
VLEALVARAIRNIEMTQEDVRLIGLSATLPNYEDVATFLRVDPAKGLFYF
DNSFRPVPLEQTYVGITEKKAIKRFQIMNEIVYEKIMEHAGKNQVLVFVH
SRKETGKTARAIRDMCLEKDTLGLFLREGSASTEVLRTEAEQCKNLELKD
LLPYGFAIHHAGMTRVDRTLVEDLFADKHIQVLVSTATLAWGVNLPAHTV
IIKGTQVYSPEKGRWTELGALDILQMLGRAGRPQYDTKGEGILITSHGEL
QYYLSLLNQQLPIESQMVSKLPDMLNAEIVLGNVQNAKDAVNWLGYAYLY
IRMLRSPTLYGISHDDLKGDPLLDQRRLDLVHTAALMLDKNNLVKYDKKT
GNFQVTELGRIASHYYITNDTVQTYNQLLKPTLSEIELFRVFSLSSEFKN
ITVREEEKLELQKLLERVPIPVKESIEEPSAKINVLLQAFISQLKLEGFA
LMADMVYVTQSAGRLMRAIFEIVLNRGWAQLTDKTLNLCKMIDKRMWQSM
CPLRQFRKLPEEVVKKIEKKNFPFERLYDLNHNEIGELIRMPKMGKTIHK
YVHLFPKLELSVHLQPITRSTLKVELTITPDFQWDEKVHGSSEAFWILVE
DVDSEVILHHEYFLLKAKYAQDEHLITFFVPVFEPLPPQYFIRVVSDRWL
SCETQLPVSFRHLILPEKYPPPTELLDLQPLPVSALRNSAFESLYQDKFP
FFNPIQTQVFNTVYNSDDNVFVGAPTGSGKTICAEFAILRMLLQSSEGRC
VYITPMEALAEQVYMDWYEKFQDRLNKKVVLLTGETSTDLKLLGKGNIII
STPEKWDILSRRWKQRKNVQNINLFVVDEVHLIGGENGPVLEVICSRMRY
ISSQIERPIRIVALSSSLSNAKDVAHWLGCSATSTFNFHPNVRPVPLELH
IQGFNISHTQTRLLSMAKPVYHAITKHSPKKPVIVFVPSRKQTRLTAIDI
LTTCAADIQRQRFLHCTEKDLIPYLEKLSDSTLKETLLNGVGYLHEGLSP
MERRLVEQLFSSGAIQVVVASRSLCWGMNVAAHLVIIMDTQYYNGKIHAY
VDYPIYDVLQMVGHANRPLQDDEGRCVIMCQGSKKDFFKKFLYEPLPVES
HLDHCMHDHFNAEIVTKTIENKQDAVDYLTWTFLYRRMTQNPNYYNLQGI
SHRHLSDHLSELVEQTLSDLEQSKCISIEDEMDVAPLNLGMIAAYYYINY
TTIELFSMSLNAKTKVRGLIEIISNAAEYENIPIRHHEDNLLRQLAQKVP
HKLNNPKFNDPHVKTNLLLQAHLSRMQLSAELQSDTEEILSKAIRLIQAC
VDVLSSNGWLSPALAAMELAQMVTQAMWSKDSYLKQLPHFTSEHIKRCTD
KGVESVFDIMEMEDEERNALLQLTDSQIADVARFCNRYPNIELSYEVVDK
DSIRSGGPVVVLVQLEREEEVTGPVIAPLFPQKREEGWWVVIGDAKSNSL
ISIKRLTLQQKAKVKLDFVAPATGAHNYTLYFMSDAYMGCDQEYKFSVD

Ligand information

>6ahd Chain I (length=136)

agcuuugcgcaguggcaguaucguagccaaugaggucuauccgaggcgcg
auuauugcuaauuacuuuucccaauaccccgccgugacgacuugcaauau
agucggcacuggcaauuuuugacagucucgagacug

...................<<<<<.<<<.....<<.....>>..>>>>>>
>>............................<<<<<<.<<<<<........
>>>>>.>>>.>>>.........<<<<<<<>>>>>>>

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6ahd Structures of the human pre-catalytic spliceosome and its precursor spliceosome.
• Resolution: 3.8 Å
• Binding residue (original residue number in PDB): R545 S546 T570 G571 D572 L575 C576 E578 H726 S727 R728 T814 V833 Y834 S835 A1079 D1119 E1212 K1213 V1214 A1243
• Binding residue (residue number reindexed from 1): R119 S120 T144 G145 D146 L149 C150 E152 H300 S301 R302 T388 V407 Y408 S409 A653 D693 E786 K787 V788 A817

Enzymatic activity

• Enzyme Commision number: 3.6.4.13: RNA helicase.

Gene Ontology

Molecular Function

• GO:0003676 nucleic acid binding
• GO:0003723 RNA binding
• GO:0003724 RNA helicase activity
• GO:0004386 helicase activity
• GO:0005515 protein binding
• GO:0005524 ATP binding
• GO:0016787 hydrolase activity
• GO:0016887 ATP hydrolysis activity
• GO:0042802 identical protein binding

Biological Process

• GO:0000354 cis assembly of pre-catalytic spliceosome
• GO:0000388 spliceosome conformational change to release U4 (or U4atac) and U1 (or U11)
• GO:0000398 mRNA splicing, via spliceosome
• GO:0001649 osteoblast differentiation
• GO:0006397 mRNA processing
• GO:0008380 RNA splicing

Cellular Component

• GO:0005634 nucleus
• GO:0005654 nucleoplasm
• GO:0005681 spliceosomal complex
• GO:0005682 U5 snRNP
• GO:0016020 membrane
• GO:0046540 U4/U6 x U5 tri-snRNP complex
• GO:0071005 U2-type precatalytic spliceosome
• GO:0071006 U2-type catalytic step 1 spliceosome
• GO:0071013 catalytic step 2 spliceosome

External links

• PDB: RCSB:6ahd, PDBe:6ahd, PDBj:6ahd
• PDBsum: 6ahd
• PubMed: 30315277
• UniProt: O75643|U520_HUMAN U5 small nuclear ribonucleoprotein 200 kDa helicase (Gene Name=SNRNP200)