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- PDB-2vw5: Structure Of The Hsp90 Inhibitor 7-O-carbamoylpremacbecin Bound T... -

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Basic information

Entry
Database: PDB / ID: 2vw5
TitleStructure Of The Hsp90 Inhibitor 7-O-carbamoylpremacbecin Bound To The N- Terminus Of Yeast Hsp90
ComponentsATP-DEPENDENT MOLECULAR CHAPERONE HSP82
KeywordsCHAPERONE / ATPASE / CYTOPLASM / INHIBITOR / ATP-BINDING / STRESS RESPONSE / NUCLEOTIDE-BINDING
Function / homology
Function and homology information


The NLRP3 inflammasome / ESR-mediated signaling / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / eNOS activation / Extra-nuclear estrogen signaling / VEGFR2 mediated vascular permeability / HSF1-dependent transactivation / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / HSF1 activation / response to oxygen levels ...The NLRP3 inflammasome / ESR-mediated signaling / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / eNOS activation / Extra-nuclear estrogen signaling / VEGFR2 mediated vascular permeability / HSF1-dependent transactivation / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / HSF1 activation / response to oxygen levels / : / protein targeting to mitochondrion / box C/D snoRNP assembly / regulation of telomere maintenance / response to osmotic stress / 'de novo' protein folding / protein maturation / proteasome assembly / Neutrophil degranulation / positive regulation of telomere maintenance via telomerase / ATP-dependent protein folding chaperone / unfolded protein binding / protein folding / cellular response to heat / protein refolding / protein stabilization / perinuclear region of cytoplasm / ATP hydrolysis activity / protein-containing complex / ATP binding / identical protein binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Heat shock protein Hsp90, conserved site / Heat shock hsp90 proteins family signature. / HSP90, C-terminal domain / Heat shock protein Hsp90, N-terminal / Heat shock protein Hsp90 family / Hsp90 protein / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase-like ATPase, C-terminal domain / Heat Shock Protein 90 / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase ...Heat shock protein Hsp90, conserved site / Heat shock hsp90 proteins family signature. / HSP90, C-terminal domain / Heat shock protein Hsp90, N-terminal / Heat shock protein Hsp90 family / Hsp90 protein / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase-like ATPase, C-terminal domain / Heat Shock Protein 90 / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase / Histidine kinase/HSP90-like ATPase superfamily / Ribosomal protein S5 domain 2-type fold / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-BC6 / ATP-dependent molecular chaperone HSP82
Similarity search - Component
Biological speciesSACCHAROMYCES CEREVISIAE (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsRoe, S.M. / Prodromou, C. / Pearl, L.H.
CitationJournal: J.Med.Chem. / Year: 2008
Title: Optimizing Natural Products by Biosynthetic Engineering: Discovery of Nonquinone Hsp90 Inhibitors.
Authors: Zhang, M.Q. / Gaisser, S. / Nur-E-Alam, M. / Sheehan, L.S. / Vousden, W.A. / Gaitatzis, N. / Peck, G. / Coates, N.J. / Moss, S.J. / Radzom, M. / Foster, T.A. / Sheridan, R.M. / Gregory, M.A. ...Authors: Zhang, M.Q. / Gaisser, S. / Nur-E-Alam, M. / Sheehan, L.S. / Vousden, W.A. / Gaitatzis, N. / Peck, G. / Coates, N.J. / Moss, S.J. / Radzom, M. / Foster, T.A. / Sheridan, R.M. / Gregory, M.A. / Roe, S.M. / Prodromou, C. / Pearl, L.H. / Boyd, S.M. / Wilkinson, B. / Martin, C.J.
History
DepositionJun 16, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 2, 2008Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ATP-DEPENDENT MOLECULAR CHAPERONE HSP82
B: ATP-DEPENDENT MOLECULAR CHAPERONE HSP82
C: ATP-DEPENDENT MOLECULAR CHAPERONE HSP82
D: ATP-DEPENDENT MOLECULAR CHAPERONE HSP82
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,70917
Polymers96,8344
Non-polymers2,87513
Water8,053447
1
A: ATP-DEPENDENT MOLECULAR CHAPERONE HSP82
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,9995
Polymers24,2091
Non-polymers7914
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: ATP-DEPENDENT MOLECULAR CHAPERONE HSP82
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,9034
Polymers24,2091
Non-polymers6953
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: ATP-DEPENDENT MOLECULAR CHAPERONE HSP82
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,9034
Polymers24,2091
Non-polymers6953
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: ATP-DEPENDENT MOLECULAR CHAPERONE HSP82
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,9034
Polymers24,2091
Non-polymers6953
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)104.193, 104.785, 109.913
Angle α, β, γ (deg.)90.00, 89.98, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-2005-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:

Ens-ID: 1 / Refine code: 4

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMETTHRTHRAA1 - 221 - 22
21METMETTHRTHRBB1 - 221 - 22
31METMETTHRTHRCC1 - 221 - 22
41METMETTHRTHRDD1 - 221 - 22
12ASNASNGLYGLYAA26 - 9426 - 94
22ASNASNGLYGLYBB26 - 9426 - 94
32ASNASNGLYGLYCC26 - 9426 - 94
42ASNASNGLYGLYDD26 - 9426 - 94
13GLYGLYGLUGLUAA100 - 214100 - 214
23GLYGLYGLUGLUBB100 - 214100 - 214
33GLYGLYGLUGLUCC100 - 214100 - 214
43GLYGLYGLUGLUDD100 - 214100 - 214

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Components

#1: Protein
ATP-DEPENDENT MOLECULAR CHAPERONE HSP82 / HSP90 / HEAT SHOCK PROTEIN HSP90 HEAT-INDUCIBLE ISOFORM / 82 KDA HEAT SHOCK PROTEIN


Mass: 24208.582 Da / Num. of mol.: 4 / Fragment: N-TERM DOMAIN, RESIDUES 1-214
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): PRSETA / References: UniProt: P02829
#2: Chemical
ChemComp-BC6 / (4E,8S,9R,10E,12S,13R,14S,16R)-13,20-dihydroxy-14-methoxy-4,8,10,12,16-pentamethyl-3-oxo-2-azabicyclo[16.3.1]docosa-1(22),4,10,18,20-pentaen-9-yl carbamate


Mass: 502.643 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C28H42N2O6
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 447 / 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: 2.88 Å3/Da / Density % sol: 57.4 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1
DetectorType: ADSC CCD / Detector: CCD / Date: Feb 19, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.77→150 Å / Num. obs: 106928 / % possible obs: 92 % / Redundancy: 3.2 % / Biso Wilson estimate: 25.38 Å2 / Rmerge(I) obs: 0.19 / Net I/σ(I): 7.1
Reflection shellResolution: 1.77→1.85 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 0.9 / % possible all: 55.3

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Processing

Software
NameVersionClassification
REFMAC5.4.0066refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1AMW

1amw


Resolution: 1.9→109.76 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.933 / SU B: 5.566 / SU ML: 0.084 / Cross valid method: THROUGHOUT / ESU R: 0.146 / ESU R Free: 0.138 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.226 4243 5 %RANDOM
Rwork0.188 ---
obs0.19 79894 90.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.37 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å2-0 Å20.49 Å2
2--0.14 Å20 Å2
3----0.13 Å2
Refinement stepCycle: LAST / Resolution: 1.9→109.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6803 0 189 447 7439
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0227175
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5412.0059702
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3035881
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.61725.247324
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.484151340
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.4951539
X-RAY DIFFRACTIONr_chiral_restr0.1040.21117
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.025283
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8021.54312
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.46127004
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.36132863
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.9774.52688
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.95 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.283 314
Rwork0.229 5993
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)
10.510.2313-0.10920.7698-0.03320.31880.0468-0.04110.0290.0275-0.043-0.0185-0.00470.0028-0.0039-0.0365-0.0131-0.0117-0.0208-0.0085-0.037933.7089-10.236742.2365
20.5198-0.19680.10670.7489-0.04350.31670.03350.0622-0.0286-0.003-0.0374-0.02740.0140.00420.0039-0.03760.0107-0.0054-0.025-0.0049-0.033233.69259.449312.7278
30.8446-0.38190.01620.73370.07960.1161-0.07110.00260.04480.05290.01630.1124-0.01910.0320.0548-0.02990.01340.0193-0.03110.0271-0.010262.4989-19.027814.8083
40.89210.4294-0.0570.67610.05180.0772-0.0774-0.0044-0.0468-0.06510.0240.09310.02120.01580.0534-0.0235-0.0145-0.0398-0.03270.023-0.012762.458318.26640.1657
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 500
2X-RAY DIFFRACTION2B1 - 500
3X-RAY DIFFRACTION3C1 - 500
4X-RAY DIFFRACTION4D1 - 500

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