Structure of PDB 3ov6 Chain A Binding Site BS01

Receptor Information

>3ov6 Chain A (length=376) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]

PIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKV
EHSDLSFSKDWSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM
GGGGEHVSFHVIQIFSFVNQSWARGQGSGWLDELQTHGWDSESGTIIFLH
QWSKGQFSNEELSDLELLFRFYLFGLTREIQDHASSKYPFEVQVKAGCEL
HSGGSPEGFFQVAFNGLDLLSFQQTTWVPSPGCGSLAQSVCHLLNHQYEG
VTETVYNLIRSTCPRFLLGLLDAGKMYVHRQVKPEAWLSSGPSPGPGRLQ
LVCHVSGFYPKPVWVMWMRGEQEQQGTQLGDILPNAQGTWYLRATLDVAD
GEAAGLSCRVKHSSLEGQDIILYWHH

Ligand information

Ligand ID

MK0

InChI

InChI=1S/C38H77O9P/c1-7-8-9-10-11-17-29(2)18-12-19-30(3)20-13-21-31(4)22-14-23-32(5)24-15-25-33(6)26-16-27-45-48(43,44)47-38-37(42)36(41)35(40)34(28-39)46-38/h29-42H,7-28H2,1-6H3,(H,43,44)/t29-,30-,31-,32-,33-,34+,35+,36-,37-,38-/m0/s1

InChIKey

BWDAWKXFHWFXEQ-RIEBCBCMSA-N

SMILES

Software	SMILES
CACTVS 3.370	CCCCCCC[CH](C)CCC[CH](C)CCC[CH](C)CCC[CH](C)CCC[CH](C)CCCO[P](O)(=O)O[CH]1O[CH](CO)[CH](O)[CH](O)[CH]1O
OpenEye OEToolkits 1.7.0	CCCCCCCC(C)CCCC(C)CCCC(C)CCCC(C)CCCC(C)CCCOP(=O)(O)OC1C(C(C(C(O1)CO)O)O)O
OpenEye OEToolkits 1.7.0	CCCCCCC[C@H](C)CCC[C@H](C)CCC[C@H](C)CCC[C@H](C)CCC[C@H](C)CCCO[P@](=O)(O)O[C@H]1[C@H]([C@H]([C@@H]([C@H](O1)CO)O)O)O
CACTVS 3.370	CCCCCCC[C@H](C)CCC[C@H](C)CCC[C@H](C)CCC[C@H](C)CCC[C@H](C)CCCO[P](O)(=O)O[C@@H]1O[C@H](CO)[C@@H](O)[C@H](O)[C@@H]1O
ACDLabs 12.01	O=P(O)(OC1OC(C(O)C(O)C1O)CO)OCCCC(C)CCCC(C)CCCC(C)CCCC(C)CCCC(C)CCCCCCC

Formula

C38 H77 O9 P

Name

1-O-[(S)-hydroxy{[(4S,8S,16S,20S)-4,8,12,16,20-pentamethylheptacosyl]oxy}phosphoryl]-beta-D-mannopyranose

PDB chain

3ov6 Chain A Residue 1105 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]

Receptor-Ligand Complex Structure

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Structure summary

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PDB	3ov6 The 2.5 A structure of CD1c in complex with a mycobacterial lipid reveals an open groove ideally suited for diverse antigen presentation
Resolution	2.502 Å
Binding residue (original residue number in PDB)	V12 Q14 G28 G39 W40 L69 F70 F72 Y73 L74 L162 C167 F170
Binding residue (residue number reindexed from 1)	V111 Q113 G127 G138 W139 L168 F169 F171 Y172 L173 L258 C263 F266
Annotation score	1

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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Cellular Component

External links

PDB	RCSB:3ov6, PDBe:3ov6, PDBj:3ov6
PDBsum	3ov6
PubMed	21167756
UniProt	P29016\|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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