Structure of PDB 4z4d Chain A Binding Site BS03

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
Ligand IDMG
InChIInChI=1S/Mg/q+2
InChIKeyJLVVSXFLKOJNIY-UHFFFAOYSA-N
SMILES
SoftwareSMILES
ACDLabs 10.04
OpenEye OEToolkits 1.5.0		[Mg+2]
CACTVS 3.341[Mg++]
FormulaMg
NameMAGNESIUM ION
ChEMBL
DrugBankDB01378
ZINC
PDB chain4z4d Chain A Residue 901 [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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PDB4z4d Water-mediated recognition of t1-adenosine anchors Argonaute2 to microRNA targets.
Resolution1.6 Å
Binding residue
(original residue number in PDB)		D597 V598
Binding residue
(residue number reindexed from 1)		D555 V556
Annotation score4
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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