Structure of PDB 5ki6 Chain A Binding Site BS01

Receptor Information
>5ki6 Chain A (length=798) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
AFKPPPRPDFGTSGRTIKLQANFFEMDIPKIDIYHYELDIKPEKCPRRVN
REIVEHMVQHFKTQIFGDRKPVFDGRKNLYTAMPLPIGRDKVELEVTLRI
FKVSIKWVSCVSLQALHDALSGRLVPFETIQALDVVMRHLPSMRYTPVGR
SFFTASNPLGGGREVWFGFHQSVRPSLWKMMLNIDVSATAFYKAQPVIEF
VCEVLDFKSIEEQQKPLTDSQRVKFTKEIKGLKVEITRKYRVCNVTRRPA
SHQTFPLQQESGQTVECTVAQYFKDRHKLVLRYPHLPCLQVGQEQKHTYL
PLEVCNIVAGQRCIKLTDNQTSTMIRATARSAPDRQEEISKLMRSADFNT
DPYVREFGIMVKDEMTDVTGRVLQPPSILYGGRNKAIATPVQGVWDMRNK
QFHTGIEIKVWAIACFAPQRQCTEVHLKSFTEQLRKISRDAGMPIQGQPC
FCKYAQGADSVEPMFRHLKNTYAGLQLVVVILPGKTPVYAEVKRVGDTVL
GMATQCVQMKNVQRTTPQTLSNLCLKINVKLGGVNNILLPQGRPPVFQQP
VIFLGADVTHPPAGDGKKPSIAAVVGSMDAHPNRYCATVRVQQHRQEIIQ
DLAAMVRELLIQFYKSTRFKPTRIIFYRDGVSEGQFQQVLHHELLAIREA
CIKLEKDYQPGITFIVVQKRHHTRLFCTDKNERVGKSGNIPAGTTVDTKI
THPTEFDFYLCSHAGIQGTSRPSHYHVLWDDNRFSSDELQILTYQLCHTY
VRCTRSVSIPAPAYYAHLVAFRARYHLHQALAKAVQVHQDTLRTMYFA
Ligand information
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB5ki6 Structure-Guided Control of siRNA Off-Target Effects.
Resolution2.153 Å
Binding residue
(original residue number in PDB)		R277 F294 Y311 H316 H336 T337 Y338 D358 T361 I365 T368 K525 Y529 K533 Q545 C546 V547 Q548 N551 T559 N562 K566 K570 R714 H753 I756 Q757 S760 R761 Y790 R792 C793 V797 S798 Y804 Y815
Binding residue
(residue number reindexed from 1)		R238 F255 Y272 H277 H297 T298 Y299 D318 T321 I325 T328 K485 Y489 K493 Q505 C506 V507 Q508 N511 T519 N522 K526 K530 R674 H713 I716 Q717 S720 R721 Y750 R752 C753 V757 S758 Y764 Y775
Binding affinityPDBbind-CN: Kd=0.16nM
Enzymatic activity
Enzyme Commision number 3.1.26.n2: argonaute-2.
Gene Ontology
Molecular Function
GO:0000340 RNA 7-methylguanosine cap binding
GO:0000993 RNA polymerase II complex binding
GO:0001046 core promoter sequence-specific DNA binding
GO:0003676 nucleic acid binding
GO:0003723 RNA binding
GO:0003725 double-stranded RNA binding
GO:0003727 single-stranded RNA binding
GO:0003729 mRNA binding
GO:0003743 translation initiation factor activity
GO:0004519 endonuclease activity
GO:0004521 RNA endonuclease activity
GO:0005515 protein binding
GO:0016891 RNA endonuclease activity, producing 5'-phosphomonoesters
GO:0035197 siRNA binding
GO:0035198 miRNA binding
GO:0035925 mRNA 3'-UTR AU-rich region binding
GO:0046872 metal ion binding
GO:0061980 regulatory RNA binding
GO:0070551 endoribonuclease activity, cleaving siRNA-paired mRNA
GO:0090624 endoribonuclease activity, cleaving miRNA-paired mRNA
GO:0098808 mRNA cap binding
Biological Process
GO:0006355 regulation of DNA-templated transcription
GO:0006412 translation
GO:0006413 translational initiation
GO:0006417 regulation of translation
GO:0009791 post-embryonic development
GO:0010501 RNA secondary structure unwinding
GO:0010586 miRNA metabolic process
GO:0010628 positive regulation of gene expression
GO:0030422 siRNA processing
GO:0031047 regulatory ncRNA-mediated gene silencing
GO:0031054 pre-miRNA processing
GO:0033962 P-body assembly
GO:0035194 regulatory ncRNA-mediated post-transcriptional gene silencing
GO:0035196 miRNA processing
GO:0035278 miRNA-mediated gene silencing by inhibition of translation
GO:0035279 miRNA-mediated gene silencing by mRNA destabilization
GO:0042985 negative regulation of amyloid precursor protein biosynthetic process
GO:0045727 positive regulation of translation
GO:0045766 positive regulation of angiogenesis
GO:0045944 positive regulation of transcription by RNA polymerase II
GO:0045947 negative regulation of translational initiation
GO:0060213 positive regulation of nuclear-transcribed mRNA poly(A) tail shortening
GO:0070922 RISC complex assembly
GO:0090128 regulation of synapse maturation
GO:0090625 siRNA-mediated gene silencing by mRNA destabilization
GO:1900153 positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay
GO:1901165 positive regulation of trophoblast cell migration
Cellular Component
GO:0000932 P-body
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0016020 membrane
GO:0016442 RISC complex
GO:0030425 dendrite
GO:0036464 cytoplasmic ribonucleoprotein granule
GO:0043232 intracellular non-membrane-bounded organelle
GO:0070062 extracellular exosome
GO:0070578 RISC-loading complex
GO:0098794 postsynapse
GO:0098978 glutamatergic synapse
GO:1990904 ribonucleoprotein complex

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:5ki6, PDBe:5ki6, PDBj:5ki6
PDBsum5ki6
PubMed27387838
UniProtQ9UKV8|AGO2_HUMAN Protein argonaute-2 (Gene Name=AGO2)

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