Structure of PDB 7qpd Chain C Binding Site BS01

Receptor Information

>7qpd Chain C (length=364) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]

VYFKEQFLDGWTSRWIESKHKSDFGKFVLSSGKFYGDEEKDKGLQTSQDA
RFYALSASFEPFSNKGQTLVVQFTVKHEQNIDCGGGYVKLFPNSLDQTDM
HGDSEYNIMFGPDICGPGTKKVHVIFNYKGKNVLINKDIRCKDDEFTHLY
TLIVRPDNTYEVKIDNSQVESGSLEDDWDFLPPKKIKDPDASKPEDWDER
AKIDDPTDSKPEDWDKPEHIPDPDAKKPEDWDEEMDGEWEPPVIQNPEYK
GEWKPRQIDNPDYKGTWIHPEIDNPEYSPDPSIYAYDNFGVLGLDLWQVK
SGTIFDNFLITNDEAYAEEFGNETWGVTKAAEKQMKDKQDEEQRLKEEEE
DKKRKEEEEAEDKE

Ligand information

Ligand ID

MAN

InChI

InChI=1S/C6H12O6/c7-1-2-3(8)4(9)5(10)6(11)12-2/h2-11H,1H2/t2-,3-,4+,5+,6+/m1/s1

InChIKey

WQZGKKKJIJFFOK-PQMKYFCFSA-N

SMILES

Software	SMILES
OpenEye OEToolkits 1.5.0	C(C1C(C(C(C(O1)O)O)O)O)O
CACTVS 3.341	OC[CH]1O[CH](O)[CH](O)[CH](O)[CH]1O
CACTVS 3.341	OC[C@H]1O[C@H](O)[C@@H](O)[C@@H](O)[C@@H]1O
OpenEye OEToolkits 1.5.0	C([C@@H]1[C@H]([C@@H]([C@@H]([C@H](O1)O)O)O)O)O
ACDLabs 10.04	OC1C(O)C(OC(O)C1O)CO

Formula

C6 H12 O6

Name

alpha-D-mannopyranose;
alpha-D-mannose;
D-mannose;
mannose

PDB chain

7qpd Chain D Residue 5 [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	7qpd Molecular basis of MHC I quality control in the peptide loading complex.
Resolution	3.73 Å
Binding residue (original residue number in PDB)	G89 D118
Binding residue (residue number reindexed from 1)	G84 D113
Annotation score	4

Enzymatic activity

Enzyme Commision number

Gene Ontology

	Molecular Function
GO:0001849	complement component C1q complex binding
GO:0003677	DNA binding
GO:0003723	RNA binding
GO:0003729	mRNA binding
GO:0005049	nuclear export signal receptor activity
GO:0005178	integrin binding
GO:0005506	iron ion binding
GO:0005509	calcium ion binding
GO:0005515	protein binding
GO:0008270	zinc ion binding
GO:0030246	carbohydrate binding
GO:0031625	ubiquitin protein ligase binding
GO:0042277	peptide binding
GO:0042562	hormone binding
GO:0044183	protein folding chaperone
GO:0046872	metal ion binding
GO:0050681	nuclear androgen receptor binding
GO:0051082	unfolded protein binding
GO:0051087	protein-folding chaperone binding
GO:0140313	molecular sequestering activity

	Biological Process
GO:0000122	negative regulation of transcription by RNA polymerase II
GO:0002502	peptide antigen assembly with MHC class I protein complex
GO:0006355	regulation of DNA-templated transcription
GO:0006457	protein folding
GO:0006611	protein export from nucleus
GO:0006874	intracellular calcium ion homeostasis
GO:0007283	spermatogenesis
GO:0008284	positive regulation of cell population proliferation
GO:0009410	response to xenobiotic stimulus
GO:0010595	positive regulation of endothelial cell migration
GO:0010628	positive regulation of gene expression
GO:0017148	negative regulation of translation
GO:0022417	protein maturation by protein folding
GO:0030866	cortical actin cytoskeleton organization
GO:0032355	response to estradiol
GO:0033144	negative regulation of intracellular steroid hormone receptor signaling pathway
GO:0033574	response to testosterone
GO:0034504	protein localization to nucleus
GO:0034975	protein folding in endoplasmic reticulum
GO:0036503	ERAD pathway
GO:0040020	regulation of meiotic nuclear division
GO:0042921	nuclear receptor-mediated glucocorticoid signaling pathway
GO:0042981	regulation of apoptotic process
GO:0045665	negative regulation of neuron differentiation
GO:0045787	positive regulation of cell cycle
GO:0045892	negative regulation of DNA-templated transcription
GO:0048387	negative regulation of retinoic acid receptor signaling pathway
GO:0050766	positive regulation of phagocytosis
GO:0050821	protein stabilization
GO:0051208	sequestering of calcium ion
GO:0055007	cardiac muscle cell differentiation
GO:0071257	cellular response to electrical stimulus
GO:0071285	cellular response to lithium ion
GO:0090398	cellular senescence
GO:0098586	cellular response to virus
GO:1900026	positive regulation of substrate adhesion-dependent cell spreading
GO:1901164	negative regulation of trophoblast cell migration
GO:1901224	positive regulation of non-canonical NF-kappaB signal transduction
GO:1901652	response to peptide
GO:1903416	response to glycoside
GO:1904614	response to biphenyl
GO:2000510	positive regulation of dendritic cell chemotaxis

	Cellular Component
GO:0001669	acrosomal vesicle
GO:0005576	extracellular region
GO:0005615	extracellular space
GO:0005634	nucleus
GO:0005635	nuclear envelope
GO:0005737	cytoplasm
GO:0005764	lysosome
GO:0005783	endoplasmic reticulum
GO:0005788	endoplasmic reticulum lumen
GO:0005789	endoplasmic reticulum membrane
GO:0005790	smooth endoplasmic reticulum
GO:0005829	cytosol
GO:0005840	ribosome
GO:0005925	focal adhesion
GO:0009897	external side of plasma membrane
GO:0009986	cell surface
GO:0012505	endomembrane system
GO:0016020	membrane
GO:0016529	sarcoplasmic reticulum
GO:0030670	phagocytic vesicle membrane
GO:0031410	cytoplasmic vesicle
GO:0032991	protein-containing complex
GO:0033018	sarcoplasmic reticulum lumen
GO:0033116	endoplasmic reticulum-Golgi intermediate compartment membrane
GO:0042824	MHC class I peptide loading complex
GO:0043231	intracellular membrane-bounded organelle
GO:0044194	cytolytic granule
GO:0044322	endoplasmic reticulum quality control compartment
GO:0048471	perinuclear region of cytoplasm
GO:0060473	cortical granule
GO:0062023	collagen-containing extracellular matrix
GO:0070062	extracellular exosome
GO:0071682	endocytic vesicle lumen
GO:0098553	lumenal side of endoplasmic reticulum membrane
GO:0098794	postsynapse
GO:0098978	glutamatergic synapse

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Cellular Component

External links

PDB	RCSB:7qpd, PDBe:7qpd, PDBj:7qpd
PDBsum	7qpd
PubMed	35948544
UniProt	P27797\|CALR_HUMAN Calreticulin (Gene Name=CALR)

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