Structure of PDB 6mrd Chain C Binding Site BS01

Receptor Information
>6mrd Chain C (length=528) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GSAKDVKFGADARALMLQGVDLLADAVAVTMGPKGRTVIIEQSWGSPKVT
KDGVTVAKSIDLKDKYKNIGAKLVQDVANNTNEEAGDGTTTATVLARSIA
KEGFEKISKGANPVEIRRGVMLAVDAVIAELKKQSKPVTTPEEIAQVATI
SANGDKEIGNIISDAMKKVGRKGVITVKDGKTLNDELEIIEGMKFDRGYI
SPYFINTSKGQKCEFQDAYVLLSEKKISSIQSIVPALEIANAHRKPLVII
AEDVDGEALSTLVLNRLKVGLQVVAVKAPGFGDNRKNQLKDMAIATGGAV
FGEEGLTLNLEDVQPHDLGKVGEVIVTKDDAMLLKGKGDKAQIEKRIQEI
IEQLDVTTSEYEKEKLNERLAKLSDGVAVLKVGGTSDVEVNEKKDRVTDA
LNATRAAVEEGIVLGGGCALLRCIPALDSLTPANEDQKIGIEIIKRTLKI
PAMTIAKNAGVEGSLIVEKIMQSSSEVGYDAMAGDFVNMVEKGIIDPTKV
VRTALLDAAGVASLLTTAEVVVTEIPKE
Ligand information
Ligand IDADP
InChIInChI=1S/C10H15N5O10P2/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(24-10)1-23-27(21,22)25-26(18,19)20/h2-4,6-7,10,16-17H,1H2,(H,21,22)(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1
InChIKeyXTWYTFMLZFPYCI-KQYNXXCUSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)OP(=O)(O)O)O)O)N
CACTVS 3.341Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
ACDLabs 10.04O=P(O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
CACTVS 3.341Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@@](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)O)O)N
FormulaC10 H15 N5 O10 P2
NameADENOSINE-5'-DIPHOSPHATE
ChEMBLCHEMBL14830
DrugBankDB16833
ZINCZINC000012360703
PDB chain6mrd Chain C Residue 601 [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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PDB6mrd Structural basis for active single and double ring complexes in human mitochondrial Hsp60-Hsp10 chaperonin.
Resolution3.82 Å
Binding residue
(original residue number in PDB)		T30 G32 P33 D87 G88 T89 T90 G416 D480 I494 D496
Binding residue
(residue number reindexed from 1)		T30 G32 P33 D87 G88 T89 T90 G416 D480 I494 D496
Annotation score5
Enzymatic activity
Catalytic site (original residue number in PDB) D52 T89 T90 D399
Catalytic site (residue number reindexed from 1) D52 T89 T90 D399
Enzyme Commision number 5.6.1.7: chaperonin ATPase.
Gene Ontology
Molecular Function
GO:0001530 lipopolysaccharide binding
GO:0002039 p53 binding
GO:0003688 DNA replication origin binding
GO:0003697 single-stranded DNA binding
GO:0003723 RNA binding
GO:0003725 double-stranded RNA binding
GO:0005515 protein binding
GO:0005524 ATP binding
GO:0008035 high-density lipoprotein particle binding
GO:0016853 isomerase activity
GO:0016887 ATP hydrolysis activity
GO:0019899 enzyme binding
GO:0031625 ubiquitin protein ligase binding
GO:0034185 apolipoprotein binding
GO:0034186 apolipoprotein A-I binding
GO:0051082 unfolded protein binding
GO:0051087 protein-folding chaperone binding
GO:0140662 ATP-dependent protein folding chaperone
Biological Process
GO:0002755 MyD88-dependent toll-like receptor signaling pathway
GO:0002842 positive regulation of T cell mediated immune response to tumor cell
GO:0006457 protein folding
GO:0006458 'de novo' protein folding
GO:0006919 activation of cysteine-type endopeptidase activity involved in apoptotic process
GO:0006986 response to unfolded protein
GO:0008637 apoptotic mitochondrial changes
GO:0009409 response to cold
GO:0032727 positive regulation of interferon-alpha production
GO:0032729 positive regulation of type II interferon production
GO:0032733 positive regulation of interleukin-10 production
GO:0032735 positive regulation of interleukin-12 production
GO:0032755 positive regulation of interleukin-6 production
GO:0034514 mitochondrial unfolded protein response
GO:0042026 protein refolding
GO:0042100 B cell proliferation
GO:0042110 T cell activation
GO:0042113 B cell activation
GO:0043032 positive regulation of macrophage activation
GO:0043065 positive regulation of apoptotic process
GO:0043066 negative regulation of apoptotic process
GO:0044406 adhesion of symbiont to host
GO:0045041 protein import into mitochondrial intermembrane space
GO:0048291 isotype switching to IgG isotypes
GO:0050821 protein stabilization
GO:0050870 positive regulation of T cell activation
GO:0051131 chaperone-mediated protein complex assembly
GO:0051604 protein maturation
GO:0051702 biological process involved in interaction with symbiont
GO:0098761 cellular response to interleukin-7
Cellular Component
GO:0005615 extracellular space
GO:0005737 cytoplasm
GO:0005739 mitochondrion
GO:0005743 mitochondrial inner membrane
GO:0005759 mitochondrial matrix
GO:0005769 early endosome
GO:0005829 cytosol
GO:0005886 plasma membrane
GO:0005905 clathrin-coated pit
GO:0009986 cell surface
GO:0016020 membrane
GO:0030135 coated vesicle
GO:0030141 secretory granule
GO:0032991 protein-containing complex
GO:0043231 intracellular membrane-bounded organelle
GO:0046696 lipopolysaccharide receptor complex
GO:0070062 extracellular exosome
GO:0097225 sperm midpiece
GO:0097524 sperm plasma membrane
GO:0140494 migrasome

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Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:6mrd, PDBe:6mrd, PDBj:6mrd
PDBsum6mrd
PubMed32317635
UniProtP10809|CH60_HUMAN 60 kDa heat shock protein, mitochondrial (Gene Name=HSPD1)

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