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

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Basic information

Entry
Database: PDB / ID: 5fpd
TitleStructure of heat shock-related 70kDA protein 2 with small-molecule ligand pyrazine-2-carboxamide (AT513) 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 / AT513.
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 / chaperone cofactor-dependent protein refolding / spermatid development ...CatSper complex / glycolipid binding / synaptonemal complex disassembly / negative regulation of inclusion body assembly / male meiotic nuclear division / synaptonemal complex / meiotic spindle / male meiosis I / chaperone cofactor-dependent protein refolding / spermatid development / response to unfolded protein / Regulation of HSF1-mediated heat shock response / Attenuation phase / protein folding chaperone / heat shock protein binding / positive regulation of G2/M transition of mitotic cell cycle / Meiotic synapsis / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / response to cold / male germ cell nucleus / ATP-dependent protein folding chaperone / PKR-mediated signaling / tau protein binding / disordered domain specific binding / unfolded protein binding / protein-folding chaperone binding / response to heat / 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
PYRAZINE-2-CARBOXAMIDE / Heat shock-related 70 kDa protein 2
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.97 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 16, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 23, 2015Group: Database references
Revision 1.2Jan 13, 2016Group: Database references
Revision 1.3Apr 6, 2016Group: Atomic model / Derived calculations / Non-polymer description
Revision 1.4Jan 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)85,0124
Polymers84,7662
Non-polymers2462
Water15,817878
1
A: HEAT SHOCK-RELATED 70KDA PROTEIN 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,5062
Polymers42,3831
Non-polymers1231
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)42,5062
Polymers42,3831
Non-polymers1231
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)48.800, 95.062, 81.779
Angle α, β, γ (deg.)90.00, 90.03, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (1, 0.00025, 0.00087), (0.00025, -1, 0.00141), (0.00087, -0.00141, -1)
Vector: 24.372, -9.224, 40.846)

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Components

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


Mass: 42383.000 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PET28B / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / References: UniProt: P54652
#2: Chemical ChemComp-PZA / PYRAZINE-2-CARBOXAMIDE / Pyrazinamide / Pyrazinamide


Mass: 123.113 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H5N3O / Comment: medication*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 878 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsPYRAZINE-2-CARBOXAMIDE (L02): ASTEX COMPOUND REGISTRY AT513. PYRAZINE-2-CARBOXAMIDE (L01): ASTEX ...PYRAZINE-2-CARBOXAMIDE (L02): ASTEX COMPOUND REGISTRY AT513. PYRAZINE-2-CARBOXAMIDE (L01): ASTEX COMPOUND REGISTRY AT513.

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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: 2.31 Å3/Da / Density % sol: 46.3 % / Description: NONE
Crystal growpH: 8
Details: 1.0M NACL, 0.1M TRIS/HCL PH=8, 20.0% W/V PEG 8000. PROTEIN CONC. = 9MG/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: May 30, 2008 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.97→38.3 Å / Num. obs: 53188 / % possible obs: 97.9 % / Observed criterion σ(I): -3.7 / Redundancy: 2 % / Biso Wilson estimate: 22.79 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 12.7
Reflection shellResolution: 1.97→2.03 Å / Rmerge(I) obs: 0.16 / Mean I/σ(I) obs: 3.7 / % possible all: 88.4

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Processing

Software
NameVersionClassification
BUSTER2.11.6refinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1S3X

1s3x


Resolution: 1.97→38.34 Å / Cor.coef. Fo:Fc: 0.9504 / Cor.coef. Fo:Fc free: 0.9179 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2229 2638 5.11 %RANDOM
Rwork0.1702 ---
obs0.1729 51667 97.9 %-
Displacement parametersBiso mean: 23.45 Å2
Baniso -1Baniso -2Baniso -3
1-0.505 Å20 Å20.0643 Å2
2--1.3281 Å20 Å2
3----1.8331 Å2
Refinement stepCycle: LAST / Resolution: 1.97→38.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5775 0 18 878 6671
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0125894HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.017963HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2078SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes157HARMONIC2
X-RAY DIFFRACTIONt_gen_planes888HARMONIC16
X-RAY DIFFRACTIONt_it5894HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion5.51
X-RAY DIFFRACTIONt_other_torsion15.66
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion802SEMIHARMONIC5
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_contact7654SEMIHARMONIC4
LS refinement shellResolution: 1.97→2.02 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2582 158 4.66 %
Rwork0.1601 3235 -
all0.1646 3393 -
obs--87.18 %
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)
11.21160.00160.15480.7544-0.16060.676-0.0287-0.0523-0.00530.01230.0045-0.03650.03330.02080.0242-0.03330.01450.0025-0.0416-0.0057-0.035627.6088-9.22052.7557
20.81680.13150.44241.15610.11721.333-0.03230.10370.1181-0.10450.00530.0507-0.0339-0.01980.027-0.01860.0065-0.0285-0.03970.0205-0.00215.45948.4589-8.0477
32.878-0.46841.61450.5933-0.03692.028-0.1731-0.25110.160.0566-0.01760.0606-0.0893-0.12180.1906-0.01840.0186-0.0019-0.0487-0.0021-0.018525.113916.227319.1195
41.21810.0375-0.18250.747-0.17440.6768-0.0270.0663-0.0053-0.0121-0.0001-0.0435-0.04110.02540.0272-0.028-0.01470.0118-0.0427-0.0059-0.037351.98280.013338.1633
50.7948-0.2344-0.50441.02920.13661.3372-0.0404-0.0899-0.12780.13350.0280.07870.0414-0.0130.0124-0.0187-0.00910.0396-0.04380.0157-0.002139.8902-17.766848.8735
62.85770.637-1.43260.8298-0.25161.8535-0.15590.2812-0.1026-0.0496-0.00470.02910.1224-0.10930.1606-0.0211-0.01870.0112-0.0418-0.0026-0.022649.5102-25.495221.7049
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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