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- PDB-5fpe: Structure of heat shock-related 70kDA protein 2 with small-molecu... -

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Basic information

Entry
Database: PDB / ID: 5fpe
TitleStructure of heat shock-related 70kDA protein 2 with small-molecule ligand 1H-1,2,4-triazol-3-amine (AT485) in an alternate binding site.
ComponentsHEAT SHOCK-RELATED 70KDA PROTEIN 2
KeywordsCHAPERONE / HEAT SHOCK-RELATED PROTEIN / HEAT SHOCK / HSP70 / HSPA2 / PROTEIN-LIGAND COMPLEX / FRAGMENT SCREENING / ALTERNATE BINDING SITE / AT485.
Function / homology
Function and homology information


CatSper complex / glycolipid binding / synaptonemal complex disassembly / negative regulation of inclusion body assembly / male meiotic nuclear division / synaptonemal complex / meiotic spindle / male meiosis I / spermatid development / chaperone cofactor-dependent protein refolding ...CatSper complex / glycolipid binding / synaptonemal complex disassembly / negative regulation of inclusion body assembly / male meiotic nuclear division / synaptonemal complex / meiotic spindle / male meiosis I / spermatid development / chaperone cofactor-dependent protein refolding / response to unfolded protein / Regulation of HSF1-mediated heat shock response / Attenuation phase / protein folding chaperone / heat shock protein binding / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / positive regulation of G2/M transition of mitotic cell cycle / Meiotic synapsis / response to cold / male germ cell nucleus / ATP-dependent protein folding chaperone / tau protein binding / PKR-mediated signaling / disordered domain specific binding / unfolded protein binding / response to heat / protein-folding chaperone binding / protein refolding / spermatogenesis / blood microparticle / positive regulation of protein phosphorylation / enzyme binding / cell surface / ATP hydrolysis activity / extracellular exosome / ATP binding / membrane / nucleus / plasma membrane / 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
3-AMINO-1,2,4-TRIAZOLE / Heat shock-related 70 kDa protein 2
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.96 Å
AuthorsJhoti, H. / Ludlow, R.F. / Patel, S. / Saini, H.K. / Tickle, I.J. / Verdonk, M.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2015
Title: Detection of Secondary Binding Sites in Proteins Using Fragment Screening.
Authors: Ludlow, R.F. / Verdonk, M.L. / Saini, H.K. / Tickle, I.J. / Jhoti, H.
History
DepositionNov 28, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 23, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 13, 2016Group: Database references
Revision 1.2Jan 10, 2024Group: 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_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_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: HEAT SHOCK-RELATED 70KDA PROTEIN 2
B: HEAT SHOCK-RELATED 70KDA PROTEIN 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,1026
Polymers84,7662
Non-polymers3364
Water16,376909
1
A: HEAT SHOCK-RELATED 70KDA PROTEIN 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,5513
Polymers42,3831
Non-polymers1682
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: HEAT SHOCK-RELATED 70KDA PROTEIN 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,5513
Polymers42,3831
Non-polymers1682
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)48.860, 94.960, 81.540
Angle α, β, γ (deg.)90.00, 89.98, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein HEAT SHOCK-RELATED 70KDA PROTEIN 2 / HEAT SHOCK 70 KDA PROTEIN 2 / HEAT SHOCK-RELATED 70KDA PROTEIN 2


Mass: 42383.000 Da / Num. of mol.: 2 / Fragment: RESIDUES 4-386
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PET28B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P54652
#2: Chemical
ChemComp-3TR / 3-AMINO-1,2,4-TRIAZOLE / AMITROLE / 3-Amino-1,2,4-triazole


Mass: 84.080 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H4N4 / Comment: inhibitor*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 909 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer details1H-1,2,4-TRIAZOL-3-AMINE (3TR): ASTEX COMPOUND REGISTRY AT485.
Sequence details3 EXTRA RESIDUES AT N TERM ARE REMAINS OF HIS TAG AFTER THROMBIN CLEAVAGE. RESIDUES 2-3 DELETED. ...3 EXTRA RESIDUES AT N TERM ARE REMAINS OF HIS TAG AFTER THROMBIN CLEAVAGE. RESIDUES 2-3 DELETED. RESIDUES 386-639 DELETED.

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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: 2.3 Å3/Da / Density % sol: 46.14 % / Description: NONE
Crystal growpH: 8
Details: 1.0M NACL, 0.1M TRIS/HCL PH=8, 20.0% W/V PEG 8000. PROTEIN CONC. = 11MG/ML.

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E / Wavelength: 1.5418
DetectorType: RIGAKU SATURN CCD / Detector: CCD / Date: Jun 6, 2008 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.96→40.8 Å / Num. obs: 53193 / % possible obs: 97.1 % / Observed criterion σ(I): -3.7 / Redundancy: 2.4 % / Biso Wilson estimate: 23.46 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 6.2
Reflection shellResolution: 1.96→2.03 Å / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 1.8 / % possible all: 84.1

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Processing

Software
NameVersionClassification
BUSTER2.11.6refinement
MOSFLMdata reduction
SCALAdata scaling
CSEARCHphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 5FPD

5fpd


Resolution: 1.96→40.77 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.9152 / SU R Cruickshank DPI: 0.183 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.205 / SU Rfree Blow DPI: 0.173 / SU Rfree Cruickshank DPI: 0.166
Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. ALL ATOMS HAVE CCP4 ATOM TYPE FROM LIBRARY
RfactorNum. reflection% reflectionSelection details
Rfree0.2329 2621 5.08 %RANDOM
Rwork0.1777 ---
obs0.1805 51605 96.61 %-
Displacement parametersBiso mean: 24.45 Å2
Baniso -1Baniso -2Baniso -3
1-0.2332 Å20 Å2-0.594 Å2
2--1.7311 Å20 Å2
3----1.9643 Å2
Refine analyzeLuzzati coordinate error obs: 0.206 Å
Refinement stepCycle: LAST / Resolution: 1.96→40.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5771 0 24 909 6704
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0125900HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.057970HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2064SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes154HARMONIC2
X-RAY DIFFRACTIONt_gen_planes892HARMONIC16
X-RAY DIFFRACTIONt_it5900HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion5.81
X-RAY DIFFRACTIONt_other_torsion15.79
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion801SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact7754SEMIHARMONIC4
LS refinement shellResolution: 1.96→2.01 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2545 144 4.84 %
Rwork0.1867 2831 -
all0.1901 2975 -
obs--75.84 %
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)
11.1177-0.02440.08590.7491-0.15520.5596-0.0264-0.0513-0.01220.0106-0.0026-0.00740.03580.00490.0289-0.03870.0098-0.0012-0.03680.0033-0.027127.6935-9.25572.7228
20.9107-0.15570.4330.84910.14791.2742-0.0260.06910.1155-0.0967-0.00520.066-0.05050.01330.0311-0.0190.0037-0.0259-0.04370.0189-0.000715.61888.5874-7.9665
32.6718-0.49091.54170.6514-0.03241.4016-0.1474-0.26060.11770.0553-0.00670.024-0.1179-0.14550.1541-0.01910.0193-0.0099-0.0347-0.0018-0.014225.143216.220519.1415
41.2185-0.026-0.08280.7467-0.22880.5988-0.01190.05550.014-0.0088-0.0171-0.0157-0.04380.02220.029-0.0362-0.01130.0031-0.0396-0.0029-0.026252.16020.014838.0686
50.78060.0337-0.50470.86580.0091.3751-0.0075-0.073-0.13430.0985-0.00330.05070.04380.0130.0107-0.0289-0.00820.0251-0.04980.0159-0.004639.9338-17.788748.7475
63.05750.457-1.92170.6183-0.04461.5419-0.1230.269-0.1845-0.0703-0.0675-0.01580.1211-0.14570.1905-0.0298-0.00490.007-0.0327-0.0026-0.003249.5527-25.260921.6303
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|4 - A|188 A|368 - A|384 }
2X-RAY DIFFRACTION2{ A|192 - A|231 A|309 - A|367 }
3X-RAY DIFFRACTION3{ A|232 - A|308 }
4X-RAY DIFFRACTION4{ B|4 - B|188 B|368 - B|384 }
5X-RAY DIFFRACTION5{ B|192 - B|231 B|309 - B|367 }
6X-RAY DIFFRACTION6{ B|232 - B|308 }

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