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- PDB-3qdd: HSP90A N-terminal domain in complex with BIIB021 -

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Entry
Database: PDB / ID: 3qdd
TitleHSP90A N-terminal domain in complex with BIIB021
ComponentsHeat shock protein HSP 90-alpha
KeywordsCHAPERONE/CHAPERONE INHIBITOR / ATPase / CHAPERONE-CHAPERONE INHIBITOR complex
Function / homology
Function and homology information


sperm mitochondrial sheath / sulfonylurea receptor binding / dATP binding / CTP binding / positive regulation of protein polymerization / Scavenging by Class F Receptors / vRNP Assembly / UTP binding / chaperone-mediated autophagy / sperm plasma membrane ...sperm mitochondrial sheath / sulfonylurea receptor binding / dATP binding / CTP binding / positive regulation of protein polymerization / Scavenging by Class F Receptors / vRNP Assembly / UTP binding / chaperone-mediated autophagy / sperm plasma membrane / Respiratory syncytial virus genome replication / Rho GDP-dissociation inhibitor binding / telomerase holoenzyme complex assembly / mitochondrial transport / Drug-mediated inhibition of ERBB2 signaling / Resistance of ERBB2 KD mutants to trastuzumab / Resistance of ERBB2 KD mutants to sapitinib / Resistance of ERBB2 KD mutants to tesevatinib / Resistance of ERBB2 KD mutants to neratinib / Resistance of ERBB2 KD mutants to osimertinib / Resistance of ERBB2 KD mutants to afatinib / Resistance of ERBB2 KD mutants to AEE788 / Resistance of ERBB2 KD mutants to lapatinib / Drug resistance in ERBB2 TMD/JMD mutants / Uptake and function of diphtheria toxin / protein import into mitochondrial matrix / TPR domain binding / dendritic growth cone / PIWI-interacting RNA (piRNA) biogenesis / Assembly and release of respiratory syncytial virus (RSV) virions / non-chaperonin molecular chaperone ATPase / protein unfolding / Sema3A PAK dependent Axon repulsion / regulation of protein ubiquitination / positive regulation of cell size / HSF1-dependent transactivation / protein folding chaperone complex / enzyme-substrate adaptor activity / response to unfolded protein / regulation of protein-containing complex assembly / HSF1 activation / Attenuation phase / neurofibrillary tangle assembly / chaperone-mediated protein complex assembly / RHOBTB2 GTPase cycle / regulation of postsynaptic membrane neurotransmitter receptor levels / axonal growth cone / telomere maintenance via telomerase / skeletal muscle contraction / positive regulation of lamellipodium assembly / nitric oxide metabolic process / response to salt stress / positive regulation of defense response to virus by host / DNA polymerase binding / eNOS activation / positive regulation of telomere maintenance via telomerase / Signaling by ERBB2 / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / cardiac muscle cell apoptotic process / endocytic vesicle lumen / positive regulation of cardiac muscle contraction / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of mitotic centrosome proteins and complexes / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / activation of innate immune response / lysosomal lumen / ESR-mediated signaling / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / positive regulation of interferon-beta production / Constitutive Signaling by Overexpressed ERBB2 / protein tyrosine kinase binding / response to cold / AURKA Activation by TPX2 / nitric-oxide synthase regulator activity / VEGFR2 mediated vascular permeability / response to cocaine / ATP-dependent protein folding chaperone / brush border membrane / Signaling by ERBB2 TMD/JMD mutants / Constitutive Signaling by EGFRvIII / Signaling by ERBB2 ECD mutants / Signaling by ERBB2 KD Mutants / positive regulation of protein import into nucleus / DDX58/IFIH1-mediated induction of interferon-alpha/beta / cellular response to virus / Regulation of actin dynamics for phagocytic cup formation / response to estrogen / Regulation of necroptotic cell death / VEGFA-VEGFR2 Pathway / extracellular matrix / tau protein binding / Downregulation of ERBB2 signaling / neuron migration / histone deacetylase binding / Chaperone Mediated Autophagy / disordered domain specific binding / positive regulation of nitric oxide biosynthetic process / Aggrephagy
Similarity search - Function
Heat shock protein Hsp90, conserved site / Heat shock hsp90 proteins family signature. / Histidine kinase-like ATPase, C-terminal domain / HSP90, C-terminal domain / Heat shock protein Hsp90, N-terminal / Heat Shock Protein 90 / Heat shock protein Hsp90 family / Hsp90 protein / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase/HSP90-like ATPase ...Heat shock protein Hsp90, conserved site / Heat shock hsp90 proteins family signature. / Histidine kinase-like ATPase, C-terminal domain / HSP90, C-terminal domain / Heat shock protein Hsp90, N-terminal / Heat Shock Protein 90 / Heat shock protein Hsp90 family / Hsp90 protein / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase/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-94M / Heat shock protein HSP 90-alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.79 Å
AuthorsArndt, J.W. / Biamonte, M.A.
CitationJournal: J.Med.Chem. / Year: 2012
Title: EC144 Is a Potent Inhibitor of the Heat Shock Protein 90.
Authors: Shi, J. / Van de Water, R. / Hong, K. / Lamer, R.B. / Weichert, K.W. / Sandoval, C.M. / Kasibhatla, S.R. / Boehm, M.F. / Chao, J. / Lundgren, K. / Timple, N. / Lough, R. / Ibanez, G. / ...Authors: Shi, J. / Van de Water, R. / Hong, K. / Lamer, R.B. / Weichert, K.W. / Sandoval, C.M. / Kasibhatla, S.R. / Boehm, M.F. / Chao, J. / Lundgren, K. / Timple, N. / Lough, R. / Ibanez, G. / Boykin, C. / Burrows, F.J. / Kehry, M.R. / Yun, T.J. / Harning, E.K. / Ambrose, C. / Thompson, J. / Bixler, S.A. / Dunah, A. / Snodgrass-Belt, P. / Arndt, J. / Enyedy, I.J. / Li, P. / Hong, V.S. / McKenzie, A. / Biamonte, M.A.
History
DepositionJan 18, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 18, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 19, 2012Group: Database references
Revision 1.2Sep 26, 2012Group: Database references
Revision 1.3Oct 5, 2022Group: Database references / Derived calculations / Structure summary
Category: chem_comp / database_2 ...chem_comp / database_2 / struct_ref_seq_dif / struct_site
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Heat shock protein HSP 90-alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,0592
Polymers26,7401
Non-polymers3191
Water4,738263
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)66.625, 91.064, 99.205
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-420-

HOH

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Components

#1: Protein Heat shock protein HSP 90-alpha / Heat shock 86 kDa / HSP86 / Renal carcinoma antigen NY-REN-38


Mass: 26739.922 Da / Num. of mol.: 1 / Fragment: N-terminal domain (UNP residues 1-236)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HSP90AA1, HSP90A, HSPC1, HSPCA / Production host: Escherichia coli (E. coli) / References: UniProt: P07900
#2: Chemical ChemComp-94M / 6-chloro-9-[(4-methoxy-3,5-dimethylpyridin-2-yl)methyl]-9H-purin-2-amine / BIIB021


Mass: 318.762 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H15ClN6O
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 263 / 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: 2.81 Å3/Da / Density % sol: 56.28 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1 M sodium cacodylate, 20% PEG2000 MME, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E DW / Wavelength: 1.54
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: May 20, 2008
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.79→49.629 Å / Num. all: 28659 / Num. obs: 28291 / % possible obs: 99 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.6 % / Rmerge(I) obs: 0.052
Reflection shellResolution: 1.79→1.85 Å / Rmerge(I) obs: 0.454 / % possible all: 97.4

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Processing

Software
NameVersionClassification
CrystalCleardata collection
MOLREPphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.79→49.629 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.945 / SU B: 3.579 / SU ML: 0.061 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.101 / ESU R Free: 0.103 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20938 1432 5.1 %RANDOM
Rwork0.17159 ---
obs0.17349 26859 98.71 %-
all-28292 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.138 Å2
Baniso -1Baniso -2Baniso -3
1--0.06 Å20 Å20 Å2
2---0.53 Å20 Å2
3---0.59 Å2
Refinement stepCycle: LAST / Resolution: 1.79→49.629 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1644 0 22 263 1929
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0221710
X-RAY DIFFRACTIONr_bond_other_d0.0010.021155
X-RAY DIFFRACTIONr_angle_refined_deg1.571.982309
X-RAY DIFFRACTIONr_angle_other_deg0.99332833
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8785212
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.1062576
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.2215319
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.246158
X-RAY DIFFRACTIONr_chiral_restr0.1040.2261
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021882
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02335
X-RAY DIFFRACTIONr_nbd_refined0.2110.2347
X-RAY DIFFRACTIONr_nbd_other0.1920.21213
X-RAY DIFFRACTIONr_nbtor_refined0.1720.2841
X-RAY DIFFRACTIONr_nbtor_other0.0850.2830
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1790.2161
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3340.214
X-RAY DIFFRACTIONr_symmetry_vdw_other0.160.215
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2280.29
X-RAY DIFFRACTIONr_mcbond_it1.2321.51370
X-RAY DIFFRACTIONr_mcbond_other0.2841.5431
X-RAY DIFFRACTIONr_mcangle_it1.39521683
X-RAY DIFFRACTIONr_scbond_it2.6783800
X-RAY DIFFRACTIONr_scangle_it3.7634.5624
LS refinement shellResolution: 1.793→1.84 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.352 93 -
Rwork0.272 1892 -
obs--94.98 %
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)
11.91640.6262-1.39090.6081-1.39694.81660.00130.19120.015-0.00790.10090.0613-0.0467-0.2805-0.1021-0.1085-0.00470.0106-0.0110.0125-0.1545-12.21927.86716.33
21.62891.0091.65131.98752.34454.1599-0.0665-0.00310.0791-0.03460.0288-0.0419-0.22460.00920.0377-0.0939-0.0041-0.0149-0.0540.0167-0.11816.31539.95926.384
33.35631.68840.60685.66792.43732.0610.0295-0.0283-0.37040.14560.1234-0.68330.18120.2122-0.1529-0.11770.02490.0065-0.05140.0282-0.095410.78225.38920.022
41.10190.1043-0.17021.57910.63030.9836-0.0191-0.12830.02380.08490.05520.0448-0.0158-0.008-0.0361-0.10070.0129-0.0034-0.02260.0333-0.135-1.69731.83228.184
58.4467-2.1238-0.57032.93010.35734.50040.01070.26860.619-0.1166-0.0249-0.006-0.2493-0.42860.0143-0.13860.0178-0.0165-0.01840.0459-0.1027-12.35938.98613.686
61.71840.62820.09121.1573-0.05461.43580.0549-0.1324-0.18770.0887-0.0065-0.12460.0656-0.0607-0.0484-0.11290.0013-0.0049-0.02670.0288-0.1306-1.58925.61927.991
72.15860.281-0.82031.5488-0.4013.2492-0.15290.188-0.2763-0.1124-0.0161-0.04410.31010.11080.169-0.10830.0060.0157-0.0137-0.0279-0.134.96223.69310.279
81.337-0.4714-0.12764.58970.2392.6665-0.00420.25550.0921-0.31720.0248-0.1845-0.0770.1077-0.0205-0.1271-0.02050.0361-0.00020.0364-0.136811.92234.4413.336
923.638910.572114.65748.15218.832210.6025-0.0336-0.1344-0.24080.06660.20830.00610.1446-0.0423-0.1746-0.11210.00440.00040.01340.0414-0.1212-2.53433.24624.817
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A17 - 42
2X-RAY DIFFRACTION2A43 - 73
3X-RAY DIFFRACTION3A74 - 87
4X-RAY DIFFRACTION4A88 - 109
5X-RAY DIFFRACTION5A110 - 138
6X-RAY DIFFRACTION6A139 - 184
7X-RAY DIFFRACTION7A185 - 207
8X-RAY DIFFRACTION8A208 - 223
9X-RAY DIFFRACTION9A999

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