Structure of PDB 6d6r Chain K Binding Site BS01

Receptor Information
>6d6r Chain K (length=853) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MLKSKTFLKKTRAGGVMKIVREHYLRDDIGCGAPGCAACGGAHEGPALEP
QPQDPQPHYLLPDTNVLLHQIDVLEDPAIRNVIVLQTVLQEVRNRSAPVY
KRIRDVTNNQEKHFYTFTNEHHRETYVEQEQGENANDRNNRAIRVAAKWY
NEHLKKMSADNQLQVIFITNDRRNKEKAIEEGIPAFTCEEYVKSLTANPE
LIDRLAIIFSEHLPLSKLQQGIKSGTYLQGTFRASRENYLEATVWIHKEI
ILQGLKHLNRAVHEDIVAVELLPKSQWKPTGRVVGIIKRNWRPYCGMLSK
SDIKESRRHLFTPADKRIPRIRIETRQASTLEGRRIIVAIDGWPRNSRYP
NGHFVRNLGDVGEKETETEVLLLEHDVPHQPFSQAVLSFLPKMPWSITEK
DMKNREDLRHLCICSVDPPGCTDINDALHCRELENGNLEVGVHIADVSHF
IRPGNALDQESARRGTTVYLCEKRIDMVPELLSSNLCSLKCDVDRLAFSC
IWEMNHNAEILKTKFTKSVINSKASLTYAEAQLRIDSANMNDDITTSLRG
LNKLAKILKKRRIEKGALTLSSPEVRFHPIDLQTKELRETNSMVEEFMLL
ANISVAKKIHEEFSEHALLRKHPAPPPSNYEILVKAARSRNLEIKTDTAK
SLAESLDQAESPTFPYLNTLLRILATRCMMQAVYFCSGMDNDFHHYGLAS
PIYTHFTSPIRRYADVIVHRLLAVAIGADCTYPELTDKHKLADICKNLNF
RHKMAQYAQRASVAFHTQLFFKSNGIVSEEAYILFVRKNAIVVLIPKYGL
EGTVFFEQLIYDDEIPSLKIEDTVFHVFDKVKVKIMLDSSNLQHQKIRMS
LVE
Ligand information
>6d6r Chain O (length=48) [Search RNA sequence] [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
tctttacggtgctcaccacaccacacacaccacaccacacaaaaaaaa
................................................
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB6d6r Helicase-Dependent RNA Decay Illuminated by a Cryo-EM Structure of a Human Nuclear RNA Exosome-MTR4 Complex.
Resolution3.45 Å
Binding residue
(original residue number in PDB)		K9 R12 I19 R21 A103 R255 Y258 S363 R370 P375 D377 K378 I380 R382 R410 Y411 P480 C483 D485 I486 N487 D488 Y531 N660 E664 R689 T745 R746 A751 H764 Y772 H774 T776 R780 R829 F874 K922
Binding residue
(residue number reindexed from 1)		K9 R12 I19 R21 A97 R236 Y239 S301 R308 P313 D315 K316 I318 R320 R348 Y349 P418 C421 D423 I424 N425 D426 Y469 N591 E595 R620 T676 R677 A682 H695 Y703 H705 T707 R711 R760 F805 K846
Enzymatic activity
Catalytic site (original residue number in PDB) D479 D485 N487 D488 Y590 R780
Catalytic site (residue number reindexed from 1) D417 D423 N425 D426 Y528 R711
Enzyme Commision number 3.1.13.-
3.1.26.-
Gene Ontology
Molecular Function
GO:0000175 3'-5'-RNA exonuclease activity
GO:0003723 RNA binding
GO:0004519 endonuclease activity
GO:0004527 exonuclease activity
GO:0004540 RNA nuclease activity
GO:0005085 guanyl-nucleotide exchange factor activity
GO:0005515 protein binding
Biological Process
GO:0000288 nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay
GO:0006364 rRNA processing
GO:0006396 RNA processing
GO:0006401 RNA catabolic process
GO:0016075 rRNA catabolic process
GO:0071031 nuclear mRNA surveillance of mRNA 3'-end processing
GO:0071034 CUT catabolic process
Cellular Component
GO:0000176 nuclear exosome (RNase complex)
GO:0000177 cytoplasmic exosome (RNase complex)
GO:0000178 exosome (RNase complex)
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005730 nucleolus
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0016020 membrane

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:6d6r, PDBe:6d6r, PDBj:6d6r
PDBsum6d6r
PubMed29906447
UniProtQ9Y2L1|RRP44_HUMAN Exosome complex exonuclease RRP44 (Gene Name=DIS3)

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