Structure of PDB 6vqy Chain D Binding Site BS01

Receptor Information
>6vqy Chain D (length=99) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
IQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVE
HSDLSFSKDWSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM
Ligand information
Ligand IDARG
InChIInChI=1S/C6H14N4O2/c7-4(5(11)12)2-1-3-10-6(8)9/h4H,1-3,7H2,(H,11,12)(H4,8,9,10)/p+1/t4-/m0/s1
InChIKeyODKSFYDXXFIFQN-BYPYZUCNSA-O
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0C(CC(C(=O)O)N)CNC(=[NH2+])N
CACTVS 3.341N[C@@H](CCCNC(N)=[NH2+])C(O)=O
OpenEye OEToolkits 1.5.0C(C[C@@H](C(=O)O)N)CNC(=[NH2+])N
CACTVS 3.341N[CH](CCCNC(N)=[NH2+])C(O)=O
ACDLabs 10.04O=C(O)C(N)CCCN\C(=[NH2+])N
FormulaC6 H15 N4 O2
NameARGININE
ChEMBL
DrugBank
ZINC
PDB chain6vqy Chain C Residue 302 [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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PDB6vqy Epitope length variants balance protective immune responses and viral escape in HIV-1 infection
Resolution2.57 Å
Binding residue
(original residue number in PDB)		S57 K58 Y63
Binding residue
(residue number reindexed from 1)		S57 K58 Y63
Annotation score4
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0005198 structural molecule activity
GO:0005515 protein binding
GO:0023026 MHC class II protein complex binding
GO:0042605 peptide antigen binding
GO:0042802 identical protein binding
GO:0042803 protein homodimerization activity
Biological Process
GO:0001913 T cell mediated cytotoxicity
GO:0001916 positive regulation of T cell mediated cytotoxicity
GO:0002237 response to molecule of bacterial origin
GO:0002474 antigen processing and presentation of peptide antigen via MHC class I
GO:0002481 antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent
GO:0002502 peptide antigen assembly with MHC class I protein complex
GO:0002503 peptide antigen assembly with MHC class II protein complex
GO:0002726 positive regulation of T cell cytokine production
GO:0006826 iron ion transport
GO:0006879 intracellular iron ion homeostasis
GO:0006955 immune response
GO:0007608 sensory perception of smell
GO:0007611 learning or memory
GO:0010977 negative regulation of neuron projection development
GO:0019885 antigen processing and presentation of endogenous peptide antigen via MHC class I
GO:0019886 antigen processing and presentation of exogenous peptide antigen via MHC class II
GO:0032092 positive regulation of protein binding
GO:0033077 T cell differentiation in thymus
GO:0034756 regulation of iron ion transport
GO:0042026 protein refolding
GO:0045646 regulation of erythrocyte differentiation
GO:0048260 positive regulation of receptor-mediated endocytosis
GO:0050680 negative regulation of epithelial cell proliferation
GO:0050768 negative regulation of neurogenesis
GO:0050778 positive regulation of immune response
GO:0050870 positive regulation of T cell activation
GO:0051289 protein homotetramerization
GO:0060586 multicellular organismal-level iron ion homeostasis
GO:0071281 cellular response to iron ion
GO:0071283 cellular response to iron(III) ion
GO:0071316 cellular response to nicotine
GO:1900121 negative regulation of receptor binding
GO:1900122 positive regulation of receptor binding
GO:1904434 positive regulation of ferrous iron binding
GO:1904437 positive regulation of transferrin receptor binding
GO:1990000 amyloid fibril formation
GO:2000774 positive regulation of cellular senescence
GO:2000978 negative regulation of forebrain neuron differentiation
Cellular Component
GO:0000139 Golgi membrane
GO:0005576 extracellular region
GO:0005615 extracellular space
GO:0005765 lysosomal membrane
GO:0005783 endoplasmic reticulum
GO:0005788 endoplasmic reticulum lumen
GO:0005794 Golgi apparatus
GO:0005829 cytosol
GO:0005886 plasma membrane
GO:0005925 focal adhesion
GO:0009897 external side of plasma membrane
GO:0009986 cell surface
GO:0012507 ER to Golgi transport vesicle membrane
GO:0016020 membrane
GO:0030670 phagocytic vesicle membrane
GO:0031901 early endosome membrane
GO:0031902 late endosome membrane
GO:0031905 early endosome lumen
GO:0035580 specific granule lumen
GO:0042612 MHC class I protein complex
GO:0042613 MHC class II protein complex
GO:0042824 MHC class I peptide loading complex
GO:0055038 recycling endosome membrane
GO:0070062 extracellular exosome
GO:1904724 tertiary granule lumen
GO:1990712 HFE-transferrin receptor complex

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Molecular Function
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Biological Process
View graph for
Cellular Component
External links
PDB RCSB:6vqy, PDBe:6vqy, PDBj:6vqy
PDBsum6vqy
PubMed
UniProtP61769|B2MG_HUMAN Beta-2-microglobulin (Gene Name=B2M)

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