Structure of PDB 5n0y Chain A Binding Site BS05

Receptor Information
>5n0y Chain A (length=635) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
QGTLIRVTPEQPTHAVCVLGTLTQLDICSSAPEDCTSFSINASPGVVVDI
AHSTWPLDPGVEVTLTMKAASGSTGDQKVQISYYGPKTPPVKALLYLTAV
EISLCADITRTGKVRTWTWGPCGQGAILLVNCDRDNLESSAMDCEDDEVL
DSEDLQDMSLMTLSTKTPKDFFTNHTLVLHVARSEMDKVRVFQATKCSVV
LGPKWPSHYLMVPGGKHNMDFYVEALAFPDTDFPGLITLTISLLDTSNLE
LPEAVVFQDSVVFRVAPWIMTPNTQPPQEVYACSIFENEDFLKSVTTLAM
KAKCKLTICPEEENMDDQWMQDEMEIGYIQAPHKTLPVVFDSPRNRGLKE
FPIKRVMGPDFGYVTRGPQTGGISGLDSFGNLEVSPPVTVRGKEYPLGRI
LFGDSCYPSNDSRQMHQALQDFLSAQQVQAPVKLYSDWLSVGHVDEFLSF
VPAPDRKGFRLLLASPRSCYKLFQEQQNEGHGEALLFEGIKKKKQQKIKN
ILSNKTLREHNSFVERCIDWNRELLKRELGLAESDIIDIPQLFKLKEFSK
AEAFFPNMVNMLVLGKHLGIPKPFGPVINGRCCLEEKVCSLLEPLGLQCT
FINDFFTYHIRHGEVHCGTNVRRKPFSFKWWNMVP
Ligand information
Ligand IDCA
InChIInChI=1S/Ca/q+2
InChIKeyBHPQYMZQTOCNFJ-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.341[Ca++]
ACDLabs 10.04
OpenEye OEToolkits 1.5.0		[Ca+2]
FormulaCa
NameCALCIUM ION
ChEMBL
DrugBankDB14577
ZINC
PDB chain5n0y Chain A Residue 706 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB5n0y Development of a Selective Inhibitor of Protein Arginine Deiminase 2.
Resolution2.23 Å
Binding residue
(original residue number in PDB)		D165 D168 E170
Binding residue
(residue number reindexed from 1)		D143 D146 E148
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) D350 H471 D473 C645
Catalytic site (residue number reindexed from 1) D322 H443 D445 C617
Enzyme Commision number 3.5.3.15: protein-arginine deiminase.
Gene Ontology
Molecular Function
GO:0004668 protein-arginine deiminase activity
GO:0005509 calcium ion binding
GO:0005515 protein binding
GO:0016787 hydrolase activity
GO:0042802 identical protein binding
GO:0046872 metal ion binding
GO:0140794 histone arginine deiminase activity
GO:0140795 histone H3R2 arginine deiminase activity
GO:0140796 histone H3R8 arginine deiminase activity
GO:0140797 histone H3R17 arginine deiminase activity
GO:0140798 histone H3R26 arginine deiminase activity
Biological Process
GO:0006325 chromatin organization
GO:0006334 nucleosome assembly
GO:0006338 chromatin remodeling
GO:0019827 stem cell population maintenance
GO:0036211 protein modification process
GO:0043687 post-translational protein modification
GO:0045087 innate immune response
Cellular Component
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0032991 protein-containing complex

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:5n0y, PDBe:5n0y, PDBj:5n0y
PDBsum5n0y
PubMed28328217
UniProtQ9UM07|PADI4_HUMAN Protein-arginine deiminase type-4 (Gene Name=PADI4)

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