Structure of PDB 4ono Chain A Binding Site BS01

Receptor Information
>4ono Chain A (length=374) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
PIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKV
EHSDLSFSKDWSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM
GGGGEHVSFHVIQIFSFVNQSWARGQGSGWLDELQTHGWDSESGTIIFLH
QWSKGQFSNEELSDLELLFRFYLFGLTREIQDHASYPFEVQVKAGCELHS
GGSPEGFFQVAFNGLDLLSFQQTTWVPSPGCGSLAQSVCHLLNHQYEGVT
ETVYNLIRSTCPRFLLGLLDAGKMYVHRQVKPEAWLSSGPSPGPGRLQLV
CHVSGFYPKPVWVMWMRGEQEQQGTQLGDILPNAQGTWYLRATLDVADGE
AAGLSCRVKHSSLEGQDIILYWHH
Ligand information
Ligand IDPMK
InChIInChI=1S/C32H67O4P/c1-7-8-9-10-11-17-28(2)18-12-19-29(3)20-13-21-30(4)22-14-23-31(5)24-15-25-32(6)26-16-27-36-37(33,34)35/h28-32H,7-27H2,1-6H3,(H2,33,34,35)/t28-,29+,30+,31+,32-/m1/s1
InChIKeyWLNOCCJMGSEDAT-GCIGRYLYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6CCCCCCCC(C)CCCC(C)CCCC(C)CCCC(C)CCCC(C)CCCOP(=O)(O)O
ACDLabs 12.01O=P(OCCCC(CCCC(C)CCCC(C)CCCC(C)CCCC(C)CCCCCCC)C)(O)O
CACTVS 3.385CCCCCCC[CH](C)CCC[CH](C)CCC[CH](C)CCC[CH](C)CCC[CH](C)CCCO[P](O)(O)=O
OpenEye OEToolkits 1.7.6CCCCCCC[C@@H](C)CCC[C@H](C)CCC[C@H](C)CCC[C@H](C)CCC[C@@H](C)CCCOP(=O)(O)O
CACTVS 3.385CCCCCCC[C@@H](C)CCC[C@H](C)CCC[C@H](C)CCC[C@H](C)CCC[C@@H](C)CCCO[P](O)(O)=O
FormulaC32 H67 O4 P
Name(4R,8S,16S,20R)-4,8,12,16,20-pentamethylheptacosyl dihydrogen phosphate
ChEMBL
DrugBank
ZINCZINC000213029846
PDB chain4ono Chain A Residue 401 [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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PDB4ono Molecular basis of mycobacterial lipid antigen presentation by CD1c and its recognition by alpha beta T cells.
Resolution2.705 Å
Binding residue
(original residue number in PDB)		V127 Q129 S144 G145 H153 W155 I162 F185 Y188 L189 L192 V274 C282
Binding residue
(residue number reindexed from 1)		V111 Q113 S128 G129 H137 W139 I146 F169 Y172 L173 L176 V253 C261
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=5.19,Kd=6.5uM
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
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Cellular Component
External links
PDB RCSB:4ono, PDBe:4ono, PDBj:4ono
PDBsum4ono
PubMed25298532
UniProtP29016|CD1B_HUMAN T-cell surface glycoprotein CD1b (Gene Name=CD1B);
P29017|CD1C_HUMAN T-cell surface glycoprotein CD1c (Gene Name=CD1C);
P61769|B2MG_HUMAN Beta-2-microglobulin (Gene Name=B2M)

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