Structure of PDB 5e84 Chain F Binding Site BS01

Receptor Information
>5e84 Chain F (length=606) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SEDVGTVVGIDLGTTYSCVGVFKNGRVEIIANDQGNRITPSYVAFTPEGE
RLIGDAAKNQLTSNPENTVFDAKRLIGRTWNDPSVQQDIKFLPFKVVEKK
TKPYIQVDIGGGQTKTFAPEEISAMVLTKMKETAEAYLGKKVTHAVVTVP
AYFNDAQRQATKDAGTIAGLNVMRIINEPTAAAIAYGLDKREGEKNILVF
DLGGGAFDVSLLTIDNGVFEVVATNGDTHLGGEDFDQRVMEHFIKLYKKK
TGKDVRKDNRAVQKLRREVEKAKRALSSQHQARIEIESFYEGEDFSETLT
RAKFEELNMDLFRSTMKPVQKVLEDSDLKKSDIDEIVLVGGSTRIPKIQQ
LVKEFFNGKEPSRGINPDEAVAYGAAVQAGVLSGDQDTGDLVLLDVCPLT
LGIETVGGVMTKLIPRNTVVPTKKSQIFSVGGTVTIKVYEGERPLTKDNH
LLGTFDLTGIPPAPRGVPQIEVTFEIDVNGILRVTAEDKGTGNKNKITIT
NDQNRLTPEEIERMVNDAEKFAEEDKKLKERIDTRNELESYAYSLKNQIG
DKEKLGGKLSSEDKETMEKAVEEKIEWLESHQDADIEDFKAKKKELEEIV
QPIISK
Ligand information
Ligand IDATP
InChIInChI=1S/C10H16N5O13P3/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(26-10)1-25-30(21,22)28-31(23,24)27-29(18,19)20/h2-4,6-7,10,16-17H,1H2,(H,21,22)(H,23,24)(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1
InChIKeyZKHQWZAMYRWXGA-KQYNXXCUSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=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[P](O)(O)=O)[CH](O)[CH]3O
ACDLabs 10.04O=P(O)(O)OP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@@](=O)(O)O[P@](=O)(O)OP(=O)(O)O)O)O)N
CACTVS 3.341Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@](O)(=O)O[P@@](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
FormulaC10 H16 N5 O13 P3
NameADENOSINE-5'-TRIPHOSPHATE
ChEMBLCHEMBL14249
DrugBankDB00171
ZINCZINC000004261765
PDB chain5e84 Chain F Residue 801 [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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PDB5e84 Close and Allosteric Opening of the Polypeptide-Binding Site in a Human Hsp70 Chaperone BiP.
Resolution2.99 Å
Binding residue
(original residue number in PDB)		G36 T37 T38 Y39 K96 G226 G227 E293 K296 R297 S300 G363 G364 R367
Binding residue
(residue number reindexed from 1)		G13 T14 T15 Y16 K73 G203 G204 E270 K273 R274 S277 G340 G341 R344
Annotation score5
Enzymatic activity
Catalytic site (original residue number in PDB) D34 K96 E201 D224
Catalytic site (residue number reindexed from 1) D11 K73 E178 D201
Enzyme Commision number 3.6.4.10: non-chaperonin molecular chaperone ATPase.
Gene Ontology
Molecular Function
GO:0005509 calcium ion binding
GO:0005515 protein binding
GO:0005524 ATP binding
GO:0016787 hydrolase activity
GO:0016887 ATP hydrolysis activity
GO:0019899 enzyme binding
GO:0019904 protein domain specific binding
GO:0031072 heat shock protein binding
GO:0031625 ubiquitin protein ligase binding
GO:0043022 ribosome binding
GO:0044183 protein folding chaperone
GO:0045296 cadherin binding
GO:0051082 unfolded protein binding
GO:0051087 protein-folding chaperone binding
GO:0051787 misfolded protein binding
GO:0140662 ATP-dependent protein folding chaperone
Biological Process
GO:0006983 ER overload response
GO:0021589 cerebellum structural organization
GO:0021680 cerebellar Purkinje cell layer development
GO:0021762 substantia nigra development
GO:0030335 positive regulation of cell migration
GO:0030512 negative regulation of transforming growth factor beta receptor signaling pathway
GO:0030968 endoplasmic reticulum unfolded protein response
GO:0031204 post-translational protein targeting to membrane, translocation
GO:0031333 negative regulation of protein-containing complex assembly
GO:0031398 positive regulation of protein ubiquitination
GO:0034975 protein folding in endoplasmic reticulum
GO:0034976 response to endoplasmic reticulum stress
GO:0035437 maintenance of protein localization in endoplasmic reticulum
GO:0036503 ERAD pathway
GO:0042026 protein refolding
GO:0042149 cellular response to glucose starvation
GO:0043066 negative regulation of apoptotic process
GO:0045944 positive regulation of transcription by RNA polymerase II
GO:0051085 chaperone cofactor-dependent protein refolding
GO:0051603 proteolysis involved in protein catabolic process
GO:0060904 regulation of protein folding in endoplasmic reticulum
GO:0071353 cellular response to interleukin-4
GO:1903891 regulation of ATF6-mediated unfolded protein response
GO:1903894 regulation of IRE1-mediated unfolded protein response
GO:1903895 negative regulation of IRE1-mediated unfolded protein response
GO:1903897 regulation of PERK-mediated unfolded protein response
Cellular Component
GO:0005634 nucleus
GO:0005737 cytoplasm
GO:0005739 mitochondrion
GO:0005783 endoplasmic reticulum
GO:0005788 endoplasmic reticulum lumen
GO:0005789 endoplasmic reticulum membrane
GO:0005793 endoplasmic reticulum-Golgi intermediate compartment
GO:0005829 cytosol
GO:0005886 plasma membrane
GO:0005925 focal adhesion
GO:0008180 COP9 signalosome
GO:0009986 cell surface
GO:0016020 membrane
GO:0030496 midbody
GO:0032991 protein-containing complex
GO:0034663 endoplasmic reticulum chaperone complex
GO:0042470 melanosome
GO:0043231 intracellular membrane-bounded organelle
GO:0070062 extracellular exosome

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:5e84, PDBe:5e84, PDBj:5e84
PDBsum5e84
PubMed26655470
UniProtP11021|BIP_HUMAN Endoplasmic reticulum chaperone BiP (Gene Name=HSPA5)

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