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- PDB-5mkr: HSP72-NBD bound to compound TCI 8 - Tyr15 in up-conformation -

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Basic information

Entry
Database: PDB / ID: 5mkr
TitleHSP72-NBD bound to compound TCI 8 - Tyr15 in up-conformation
ComponentsHeat shock 70 kDa protein 1A
KeywordsCHAPERONE / Irreversible Inhibitor / Lysine modification
Function / homology
Function and homology information


positive regulation of endoribonuclease activity / denatured protein binding / cellular heat acclimation / negative regulation of inclusion body assembly / death receptor agonist activity / Viral RNP Complexes in the Host Cell Nucleus / C3HC4-type RING finger domain binding / positive regulation of nucleotide-binding oligomerization domain containing 2 signaling pathway / positive regulation of microtubule nucleation / ATP-dependent protein disaggregase activity ...positive regulation of endoribonuclease activity / denatured protein binding / cellular heat acclimation / negative regulation of inclusion body assembly / death receptor agonist activity / Viral RNP Complexes in the Host Cell Nucleus / C3HC4-type RING finger domain binding / positive regulation of nucleotide-binding oligomerization domain containing 2 signaling pathway / positive regulation of microtubule nucleation / ATP-dependent protein disaggregase activity / misfolded protein binding / negative regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway / positive regulation of tumor necrosis factor-mediated signaling pathway / regulation of mitotic spindle assembly / transcription regulator inhibitor activity / lysosomal transport / aggresome / cellular response to steroid hormone stimulus / mRNA catabolic process / chaperone cofactor-dependent protein refolding / regulation of protein ubiquitination / HSF1-dependent transactivation / response to unfolded protein / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / chaperone-mediated protein complex assembly / cellular response to unfolded protein / Regulation of HSF1-mediated heat shock response / Attenuation phase / negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / ATP metabolic process / inclusion body / heat shock protein binding / negative regulation of protein ubiquitination / protein folding chaperone / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / centriole / positive regulation of erythrocyte differentiation / positive regulation of RNA splicing / positive regulation of interleukin-8 production / AUF1 (hnRNP D0) binds and destabilizes mRNA / G protein-coupled receptor binding / ATP-dependent protein folding chaperone / negative regulation of transforming growth factor beta receptor signaling pathway / negative regulation of cell growth / PKR-mediated signaling / histone deacetylase binding / transcription corepressor activity / disordered domain specific binding / unfolded protein binding / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / positive regulation of NF-kappaB transcription factor activity / virus receptor activity / cellular response to heat / cellular response to oxidative stress / protein refolding / vesicle / blood microparticle / ficolin-1-rich granule lumen / protein stabilization / receptor ligand activity / nuclear speck / cadherin binding / ribonucleoprotein complex / negative regulation of cell population proliferation / signaling receptor binding / focal adhesion / centrosome / ubiquitin protein ligase binding / Neutrophil degranulation / positive regulation of gene expression / negative regulation of apoptotic process / perinuclear region of cytoplasm / negative regulation of transcription by RNA polymerase II / enzyme binding / endoplasmic reticulum / ATP hydrolysis activity / protein-containing complex / mitochondrion / RNA binding / extracellular space / extracellular exosome / extracellular region / nucleoplasm / ATP binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Defensin A-like - #30 / Defensin A-like / Heat shock hsp70 proteins family signature 2. / Heat shock hsp70 proteins family signature 1. / Heat shock hsp70 proteins family signature 3. / Heat shock protein 70, conserved site / Heat shock protein 70kD, peptide-binding domain superfamily / Heat shock protein 70 family / Hsp70 protein / Heat shock protein 70kD, C-terminal domain superfamily ...Defensin A-like - #30 / Defensin A-like / Heat shock hsp70 proteins family signature 2. / Heat shock hsp70 proteins family signature 1. / Heat shock hsp70 proteins family signature 3. / Heat shock protein 70, conserved site / Heat shock protein 70kD, peptide-binding domain superfamily / Heat shock protein 70 family / Hsp70 protein / Heat shock protein 70kD, C-terminal domain superfamily / ATPase, substrate binding domain, subdomain 4 / Actin; Chain A, domain 4 / ATPase, nucleotide binding domain / ATPase, nucleotide binding domain / Nucleotidyltransferase; domain 5 / Alpha-Beta Complex / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
CITRATE ANION / Chem-TI8 / Heat shock 70 kDa protein 1A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.87 Å
AuthorsPettinger, J. / Westwood, I.M. / Cronin, N. / Le Bihan, Y.-V. / Van Montfort, R.L.M.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Cancer Research UKC309/A8274 United Kingdom
Cancer Research UKC309/A11566 United Kingdom
CitationJournal: Angew. Chem. Int. Ed. Engl. / Year: 2017
Title: An Irreversible Inhibitor of HSP72 that Unexpectedly Targets Lysine-56.
Authors: Pettinger, J. / Le Bihan, Y.V. / Widya, M. / van Montfort, R.L. / Jones, K. / Cheeseman, M.D.
History
DepositionDec 5, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 1, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 29, 2017Group: Database references
Revision 1.2May 1, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Heat shock 70 kDa protein 1A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,8743
Polymers43,1961
Non-polymers6782
Water13,908772
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area300 Å2
ΔGint2 kcal/mol
Surface area17370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.677, 86.400, 100.232
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 Heat shock 70 kDa protein 1A / Heat shock 70 kDa protein 1 / HSP70.1


Mass: 43195.902 Da / Num. of mol.: 1 / Fragment: UNP residues 1-380
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HSPA1A, HSPA1, HSX70 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P0DMV8
#2: Chemical ChemComp-TI8 / 3-[(2~{R},3~{S},4~{R},5~{R})-5-[6-azanyl-8-[(4-chlorophenyl)methylamino]purin-9-yl]-3,4-bis(oxidanyl)oxolan-2-yl]propyl prop-2-enoate


Mass: 488.924 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H25ClN6O5
#3: Chemical ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5O7
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 772 / 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: 2.54 Å3/Da / Density % sol: 51.57 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4.1
Details: 16% w/v PEG-3350, 0.06 M citric acid, 0.04 M BIS-TRIS propane. Inhibitor was pre-incubated with protein prior to co-crystallisation.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-X / Wavelength: 1.5419 Å
DetectorType: DECTRIS PILATUS 300K / Detector: PIXEL / Date: Oct 27, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5419 Å / Relative weight: 1
ReflectionResolution: 1.87→86.4 Å / Num. obs: 35583 / % possible obs: 95.2 % / Redundancy: 8.9 % / Biso Wilson estimate: 15.62 Å2 / CC1/2: 0.999 / Rpim(I) all: 0.018 / Net I/σ(I): 37.1
Reflection shellResolution: 1.87→1.97 Å / Redundancy: 2.9 % / Mean I/σ(I) obs: 4.8 / CC1/2: 0.934 / Rpim(I) all: 0.163 / % possible all: 69.4

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
PHASERphasing
XDSdata reduction
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: In-house

Resolution: 1.87→34.98 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.911 / SU R Cruickshank DPI: 0.139 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.176 / SU Rfree Blow DPI: 0.156 / SU Rfree Cruickshank DPI: 0.14
RfactorNum. reflection% reflectionSelection details
Rfree0.222 1777 5.07 %RANDOM
Rwork0.165 ---
obs0.167 35051 94.4 %-
Displacement parametersBiso mean: 18.02 Å2
Baniso -1Baniso -2Baniso -3
1-1.3713 Å20 Å20 Å2
2---1.3894 Å20 Å2
3---0.0181 Å2
Refine analyzeLuzzati coordinate error obs: 0.19 Å
Refinement stepCycle: 1 / Resolution: 1.87→34.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2954 0 47 772 3773
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.013098HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.014204HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1097SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes82HARMONIC2
X-RAY DIFFRACTIONt_gen_planes483HARMONIC5
X-RAY DIFFRACTIONt_it3098HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.13
X-RAY DIFFRACTIONt_other_torsion15.33
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion419SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies34HARMONIC1
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact4453SEMIHARMONIC4
LS refinement shellResolution: 1.87→1.92 Å / Rfactor Rfree error: 0 / Total num. of bins used: 18
RfactorNum. reflection% reflection
Rfree0.415 111 6.07 %
Rwork0.319 1719 -
all0.324 1830 -
obs--61.37 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.76520.74670.15281.1213-0.42361.64210.0127-0.0012-0.02120.10390.04750.25540.0372-0.1707-0.0603-0.0222-0.01080.0149-0.03470.00350.0007-15.320212.5091-17.3099
21.7574-0.4484-0.00930.87960.0991.15530.0083-0.2338-0.02130.3572-0.00820.04070.18620.0775-0.00010.06920.00610.0005-0.0058-0.005-0.0862-2.395516.3167-6.0591
31.0909-0.38510.4831.43070.31860-0.0412-0.07560.12830.18950.0148-0.1517-0.1253-0.10850.02640.00190.0026-0.0312-0.00390.0008-0.03496.563821.6415-13.3657
41.8882-0.1356-0.89912.2909-0.58584.58950.0637-0.01480.25070.0220.0254-0.3598-0.07210.2915-0.0891-0.0796-0.0069-0.0066-0.01780.01830.016914.103620.283-16.918
50.35420.2434-0.18160.5484-0.12150.56280.0057-0.0655-0.05220.0561-0.04710.00230.09460.0820.04140.02640.0244-0.0005-0.03050.0079-0.0397-2.466910.6781-16.5393
60-0.078-0.2680.7949-0.14630.32680.0090.0366-0.0148-0.1319-0.04110.04990.0943-0.01670.0320.02320.00230.0036-0.02320.0006-0.0426-4.814112.1926-26.8743
72.19050.4532-0.79432.14440.66332.1287-0.04490.2219-0.1342-0.13240.08830.13270.2957-0.1636-0.04340.04050.0034-0.0343-0.05080.0067-0.0785-12.03426.1595-32.4937
81.72631.44542.54530.5002-1.47582.34920.02990.00860.08970.1465-0.0136-0.1922-0.12090.1112-0.0162-0.0152-0.0010.0066-0.02480.0094-0.06450.608645.7383-7.7689
92.8786-0.02142.89631.0095-0.20494.2745-0.06510.0023-0.02130.1230.0205-0.0612-0.01120.08770.04460.04050.00830.0155-0.04550.0113-0.0869-1.827141.6559-1.2186
100.5014-0.12740.31030.67010.55292.21590.0183-0.02030.0049-0.0531-0.0190.00510.0167-0.03960.0006-0.0140.0015-0.0003-0.05610.0177-0.0818-9.75139.7903-24.814
110.09510.0262-0.03142.1383-0.35870.3157-0.0196-0.0175-0.04530.00510.03340.1859-0.0048-0.0901-0.0138-0.0102-0.0027-0.00510.00290.00240.0037-17.549326.1149-25.7414
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{A|1 - 28}
2X-RAY DIFFRACTION2{A|29 - 52}
3X-RAY DIFFRACTION3{A|53 - 80}
4X-RAY DIFFRACTION4{A|81 - 109}
5X-RAY DIFFRACTION5{A|110 - 151}
6X-RAY DIFFRACTION6{A|152 - 182}
7X-RAY DIFFRACTION7{A|183 - 229}
8X-RAY DIFFRACTION8{A|230 - 249}
9X-RAY DIFFRACTION9{A|250 - 292}
10X-RAY DIFFRACTION10{A|293 - 343}
11X-RAY DIFFRACTION11{A|344 - 385}

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