Structure of PDB 6d6r Chain K Binding Site BS02

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
Ligand IDZN
InChIInChI=1S/Zn/q+2
InChIKeyPTFCDOFLOPIGGS-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.341[Zn++]
ACDLabs 10.04
OpenEye OEToolkits 1.5.0		[Zn+2]
FormulaZn
NameZINC ION
ChEMBLCHEMBL1236970
DrugBankDB14532
ZINC
PDB chain6d6r Chain K Residue 1001 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
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)		C31 C36 C39 H159
Binding residue
(residue number reindexed from 1)		C31 C36 C39 H153
Annotation score4
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
View graph for
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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