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- PDB-6baw: Structure of GRP94 with a selective resorcinylic inhibitor. -

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Basic information

Entry
Database: PDB / ID: 6baw
TitleStructure of GRP94 with a selective resorcinylic inhibitor.
ComponentsEndoplasmin
KeywordsCHAPERONE/INHIBITOR / CHAPERONE-INHIBITOR complex
Function / homology
Function and homology information


Trafficking and processing of endosomal TLR / Scavenging by Class A Receptors / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / Interleukin-4 and Interleukin-13 signaling / Post-translational protein phosphorylation / sarcoplasmic reticulum lumen / ERAD pathway / ATP-dependent protein folding chaperone / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / unfolded protein binding ...Trafficking and processing of endosomal TLR / Scavenging by Class A Receptors / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / Interleukin-4 and Interleukin-13 signaling / Post-translational protein phosphorylation / sarcoplasmic reticulum lumen / ERAD pathway / ATP-dependent protein folding chaperone / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / unfolded protein binding / melanosome / protein folding / perinuclear region of cytoplasm / endoplasmic reticulum / ATP hydrolysis activity / ATP binding
Similarity search - Function
Endoplasmic reticulum targeting sequence. / Heat shock protein Hsp90, conserved site / Heat shock hsp90 proteins family signature. / HSP90, C-terminal domain / Histidine kinase-like ATPase, C-terminal domain / Heat shock protein Hsp90, N-terminal / Heat shock protein Hsp90 family / Hsp90 protein / Heat Shock Protein 90 / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase ...Endoplasmic reticulum targeting sequence. / Heat shock protein Hsp90, conserved site / Heat shock hsp90 proteins family signature. / HSP90, C-terminal domain / Histidine kinase-like ATPase, C-terminal domain / Heat shock protein Hsp90, N-terminal / Heat shock protein Hsp90 family / Hsp90 protein / Heat Shock Protein 90 / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase superfamily / Ribosomal protein S5 domain 2-type fold / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-D57 / PHOSPHATE ION / Endoplasmin
Similarity search - Component
Biological speciesCanis lupus familiaris (dog)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.703 Å
AuthorsQue, N.L.S. / Gewirth, D.T.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)R01-CA095130 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)P01-CA186866 United States
CitationJournal: J. Med. Chem. / Year: 2018
Title: Structure Based Design of a Grp94-Selective Inhibitor: Exploiting a Key Residue in Grp94 To Optimize Paralog-Selective Binding.
Authors: Que, N.L.S. / Crowley, V.M. / Duerfeldt, A.S. / Zhao, J. / Kent, C.N. / Blagg, B.S.J. / Gewirth, D.T.
History
DepositionOct 16, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 18, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 25, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Feb 20, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Endoplasmin
A: Endoplasmin
C: Endoplasmin
D: Endoplasmin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,04526
Polymers106,0564
Non-polymers2,98922
Water3,189177
1
B: Endoplasmin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,2396
Polymers26,5141
Non-polymers7245
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Endoplasmin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,3638
Polymers26,5141
Non-polymers8497
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Endoplasmin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,2066
Polymers26,5141
Non-polymers6925
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Endoplasmin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,2396
Polymers26,5141
Non-polymers7245
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
B: Endoplasmin
C: Endoplasmin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,44412
Polymers53,0282
Non-polymers1,41610
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3130 Å2
ΔGint-26 kcal/mol
Surface area20700 Å2
MethodPISA
6
A: Endoplasmin
D: Endoplasmin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,60114
Polymers53,0282
Non-polymers1,57312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3500 Å2
ΔGint-25 kcal/mol
Surface area20830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.647, 93.710, 175.408
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Endoplasmin / 94 kDa glucose-regulated protein / GRP-94 / Heat shock protein 90 kDa beta member 1


Mass: 26514.012 Da / Num. of mol.: 4
Mutation: RESIDUES 287-327 DELETED AND REPLACED WITH 4 GLYCINES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Canis lupus familiaris (dog) / Gene: HSP90B1, GRP94, TRA1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P41148
#2: Chemical
ChemComp-D57 / dimethyl 2-[2-(1-benzyl-1H-imidazol-2-yl)ethyl]-4,6-dihydroxybenzene-1,3-dicarboxylate


Mass: 410.420 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C22H22N2O6 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 177 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.63 Å3/Da / Density % sol: 66.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: Peg 2000 MME, Ammonium phosphate, Sodium Cacodylate pH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0333 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 12, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0333 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 41640 / % possible obs: 96.8 % / Redundancy: 5.9 % / Net I/σ(I): 9
Reflection shellResolution: 2.7→2.75 Å / Num. measured obs: 2119 / Rsym value: 1

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Processing

Software
NameVersionClassification
PHENIX(1.12rc0_2784: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.703→41.903 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.38
RfactorNum. reflection% reflection
Rfree0.2574 1993 4.79 %
Rwork0.2137 --
obs0.2158 41569 96.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.703→41.903 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6665 0 199 177 7041
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0026959
X-RAY DIFFRACTIONf_angle_d0.4619381
X-RAY DIFFRACTIONf_dihedral_angle_d6.5614543
X-RAY DIFFRACTIONf_chiral_restr0.0391068
X-RAY DIFFRACTIONf_plane_restr0.0021171
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7028-2.77040.36021400.30322749X-RAY DIFFRACTION96
2.7704-2.84530.30591460.28152840X-RAY DIFFRACTION98
2.8453-2.9290.33531430.2852857X-RAY DIFFRACTION98
2.929-3.02350.34781450.26692835X-RAY DIFFRACTION98
3.0235-3.13150.31440.26342821X-RAY DIFFRACTION98
3.1315-3.25690.26881430.23892828X-RAY DIFFRACTION98
3.2569-3.4050.3171440.24052817X-RAY DIFFRACTION98
3.405-3.58450.25521440.22062835X-RAY DIFFRACTION97
3.5845-3.80890.25671450.19452802X-RAY DIFFRACTION97
3.8089-4.10270.26441360.18682828X-RAY DIFFRACTION96
4.1027-4.51520.20361420.16552813X-RAY DIFFRACTION96
4.5152-5.16750.21271430.15742831X-RAY DIFFRACTION96
5.1675-6.50660.2291370.2142833X-RAY DIFFRACTION95
6.5066-41.90780.21561410.20912887X-RAY DIFFRACTION92

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