Structure of PDB 4z4d Chain A Binding Site BS01

Receptor Information
>4z4d Chain A (length=803) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
AFKPPPRPDFGTSGRTIKLQANFFEMDIPKIDIYHYELDIKPEKCPRRVN
REIVEHMVQHFKTQIFGDRKPVFDGRKNLYTAMPLPIGRDKVELEVTLPI
FKVSIKWVSCVSLQALHDALSGRLPSVPFETIQALDVVMRHLPSMRYTPV
GRSFFTASEGCSNPLGGGREVWFGFHQSVRPSLWKMMLNIDVSATAFYKA
QPVIEFVCEVLDFKSIEEQQKPLTDSQRVKFTKEIKGLKVEIKRKYRVCN
VTRRPASHQTFPECTVAQYFKDRHKLVLRYPHLPCLQVGQEQKHTYLPLE
VCNIVAGQRCIKKLTDNQTSTMIRATARSAPDRQEEISKLMRSADFNTDP
YVREFGIMVKDEMTDVTGRVLQPPSILYGGRNKAIATPVQGVWDMRNKQF
HTGIEIKVWAIACFAPQRQCTEVHLKSFTEQLRKISRDAGMPIQGQPCFC
KYAQGADSVEPMFRHLKNTYAGLQLVVVILPGKTPVYAEVKRVGDTVLGM
ATQCVQMKNVQRTTPQTLSNLCLKINVKLGGVNNILLPQGRPPVFQQPVI
FLGADVTHPPAGDGKKPSIAAVVGSMDAHPNRYCATVRVQQHRQEIIQDL
AAMVRELLIQFYKSTRFKPTRIIFYRDGVSEGQFQQVLHHELLAIREACI
KLEKDYQPGITFIVVQKRHHTRLFCTDKNERVGKSGNIPAGTTVDTKITH
PTEFDFYLCSHAGIQGTSRPSHYHVLWDDNRFSSDELQILTYQLCHTYVR
CTRSVSIPAPAYYAHLVAFRARYHLVDKEGRDHQALAKAVQVHQDTLRTM
YFA
Ligand information
>4z4d Chain B (length=20) [Search RNA sequence] [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
uucacauugcccaagucuuu
....................
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB4z4d Water-mediated recognition of t1-adenosine anchors Argonaute2 to microRNA targets.
Resolution1.6 Å
Binding residue
(original residue number in PDB)		P67 R68 V70 R97 V177 G178 R179 R277 F294 Y311 H316 H336 T337 Y338 I365 L522 G524 K525 T526 Y529 K533 Q545 C546 V547 Q548 N551 T559 N562 L563 K566 K570 H600 P601 P602 A603 R635 E637 S672 Q675 K709 R710 H753 I756 Q757 S760 R761 Y790 R792 C793 R795 S798 Y804
Binding residue
(residue number reindexed from 1)		P46 R47 V49 R76 V150 G151 R152 R244 F261 Y269 H274 H294 T295 Y296 I323 L480 G482 K483 T484 Y487 K491 Q503 C504 V505 Q506 N509 T517 N520 L521 K524 K528 H558 P559 P560 A561 R593 E595 S630 Q633 K667 R668 H711 I714 Q715 S718 R719 Y748 R750 C751 R753 S756 Y762
Binding affinityPDBbind-CN: Kd=1.9nM
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:4z4d, PDBe:4z4d, PDBj:4z4d
PDBsum4z4d
PubMed26359634
UniProtQ9UKV8|AGO2_HUMAN Protein argonaute-2 (Gene Name=AGO2)

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