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3atu

Crystal structure of human Hsp70 NBD in the ADP- and Mg ion-bound state

Method: X-RAY DIFFRACTION Dmax: 70.8 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Heat shock 70 kDa protein 1A/1B

Homo sapiens

UniProt P08107

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain A； UniProt 1–388 Fragment：Nucleotide-binding domain (UNP RESIDUES 1-388) ADP ADENOSINE-5'-DIPHOSPHATE × 1 PO4 PHOSPHATE ION × 1 MG MAGNESIUM ION × 1 NA SODIUM ION × 1 PG0 2-(2-METHOXYETHOXY)ETHANOL × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；0.1M HEPES-NaOH (pH 7.0), 0.15M MgCl2, 30 % PEG MME 500, VAPOR DIFFUSION, SITTING DROP, temperature 293K Resolution 1.65 Å R-free 0.218

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 3ATU Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1HJO ATPase domain of human heat shock 70kDa protein 1 Deposited 1998-10-13 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 3–382（380 aa） Fragment：42KD ATPASE N-TERMINAL FRAGMENT
Not recorded CA CALCIUM ION × 1 CL CHLORIDE ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7；8% PEG-8000 25 MM IMIDAZOLE, PH 7.0 20MM CACL2 1MM GAMMA-S-ATP
Resolution 2.30 Å R-free 0.253
1S3X The crystal structure of the human Hsp70 ATPase domain Deposited 2004-01-14 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–382（382 aa） Fragment：ATPASE DOMAIN
Not recorded PO4 PHOSPHATE ION × 1 CA CALCIUM ION × 2 NA SODIUM ION × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；imidazole buffer, PEG 8000, CaCl2, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 1.84 Å R-free 0.219
1XQS Crystal structure of the HspBP1 core domain complexed with the fragment of Hsp70 ATPase domain Deposited 2004-10-13 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 184–371（188 aa） Fragment：LOBE II OF ATPASE DOMAIN (184-371)
Not recorded AMP ADENOSINE MONOPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；PEG8000, Potassium chloride, Magnesium chloride, AMP-PNP, DTT, HEPES KOH, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.90 Å R-free 0.296
1XQS Crystal structure of the HspBP1 core domain complexed with the fragment of Hsp70 ATPase domain Deposited 2004-10-13 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 184–371（188 aa） Fragment：LOBE II OF ATPASE DOMAIN (184-371)
Not recorded AMP ADENOSINE MONOPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；PEG8000, Potassium chloride, Magnesium chloride, AMP-PNP, DTT, HEPES KOH, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.90 Å R-free 0.296
2LMG Solution Structure of The C-terminal Domain (537-610) of Human Heat Shock Protein 70 Deposited 2011-12-01 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 537–610（74 aa） Fragment：UNP residues 537-610
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.5；298 K；Pressure ambient
NMR sample composition 1 mM [U-100% 15N] protein-1, 20 mM sodium phosphate-2, 50 mM sodium chloride-3, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 1 mM [U-100% 13C; U-100% 15N] protein-4, 20 mM sodium phosphate-5, 50 mM sodium chloride-6, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 1 mM [U-100% 13C; U-100% 15N] protein-7, 20 mM sodium phosphate-8, 50 mM sodium chloride-9, 100% D2O | 100% D2O
Resolution not provided
3A8Y Crystal structure of the complex between the BAG5 BD5 and Hsp70 NBD Deposited 2009-10-13 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–388（388 aa） Fragment：Nucleotide-binding domain, UNP residues 1-388
Not recorded TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；0.1M Tris-HCL, 0.25M Trimethylamine n-oxide, 20% PEG MME 2000, 3% Hexanediol , pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.30 Å R-free 0.281
3A8Y Crystal structure of the complex between the BAG5 BD5 and Hsp70 NBD Deposited 2009-10-13 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–388（388 aa） Fragment：Nucleotide-binding domain, UNP residues 1-388
Not recorded TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；0.1M Tris-HCL, 0.25M Trimethylamine n-oxide, 20% PEG MME 2000, 3% Hexanediol , pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.30 Å R-free 0.281
3ATV Crystal structure of human Hsp70 NBD in the ADP-bound and Mg ion-free state Deposited 2011-01-13 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–388（388 aa） Fragment：Nucleotide-binding domain (UNP RESIDUES 1-388)
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 K POTASSIUM ION × 1 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；293 K；0.1M Bis-Tris (pH 5.5), 0.25M KNO3, 25% PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 1.58 Å R-free 0.208
3AY9 Crystal structure of human Hsp70 NBD in the ADP-, Mg ion-, and K ion-bound state Deposited 2011-05-03 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–388（388 aa） Fragment：nucleotide-binding domain (UNP RESIDUES 1-388)
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 PO4 PHOSPHATE ION × 1 MG MAGNESIUM ION × 1 K POTASSIUM ION × 1 CL CHLORIDE ION × 1 CA CALCIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.7；293 K；0.05M calcium chloride, 0.1M bis-tris (pH6.5), 30% PEG MME 550, pH 5.7, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 1.75 Å R-free 0.213
3D2E Crystal structure of a complex of Sse1p and Hsp70, Selenomethionine-labeled crystals Deposited 2008-05-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–382（382 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) MG MAGNESIUM ION × 1 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；277 K；17 % (w/v) polyethyleneglycol-6000, 50 mM KCl, 100 mM HEPES-KOH pH 7.5, vapor diffusion, temperature 277K
Resolution 2.35 Å R-free 0.262
3D2E Crystal structure of a complex of Sse1p and Hsp70, Selenomethionine-labeled crystals Deposited 2008-05-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 1–382（382 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) MG MAGNESIUM ION × 1 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；277 K；17 % (w/v) polyethyleneglycol-6000, 50 mM KCl, 100 mM HEPES-KOH pH 7.5, vapor diffusion, temperature 277K
Resolution 2.35 Å R-free 0.262
3D2F Crystal structure of a complex of Sse1p and Hsp70 Deposited 2008-05-08 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–382（382 aa）
Not recorded MG MAGNESIUM ION × 3 K POTASSIUM ION × 1 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 8；277 K；15 % (w/v) polyethyleneglycol-6000, 100 mM Tris-HCl pH 8.0, 10 mM DTT, VAPOR DIFFUSION, temperature 277K
Resolution 2.30 Å R-free 0.244
3D2F Crystal structure of a complex of Sse1p and Hsp70 Deposited 2008-05-08 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 1–382（382 aa）
Not recorded MG MAGNESIUM ION × 3 K POTASSIUM ION × 1 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 8；277 K；15 % (w/v) polyethyleneglycol-6000, 100 mM Tris-HCl pH 8.0, 10 mM DTT, VAPOR DIFFUSION, temperature 277K
Resolution 2.30 Å R-free 0.244
3JXU Crystal structure of the human 70kDa heat shock protein 1A (Hsp70-1) ATPase domain in complex with ADP and inorganic phosphate Deposited 2009-09-21 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–387（387 aa） Fragment：ATPase domain, UNP resiudes 1-387
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 PO4 PHOSPHATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；277 K；0.2M magnesium chloride hexahydrate, 0.1M bis-tris, 25% PEG 3350, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Resolution 2.14 Å R-free 0.262
3LOF C-terminal domain of human heat shock 70kDa protein 1B. Deposited 2010-02-03 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 534–641（108 aa） Fragment：C-terminal domain
Chain B 534–641（108 aa） Fragment：C-terminal domain
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；294 K；2.4 M sodium malonate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Resolution 2.40 Å R-free 0.235
3LOF C-terminal domain of human heat shock 70kDa protein 1B. Deposited 2010-02-03 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain C 534–641（108 aa） Fragment：C-terminal domain
Chain D 534–641（108 aa） Fragment：C-terminal domain
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；294 K；2.4 M sodium malonate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Resolution 2.40 Å R-free 0.235
3LOF C-terminal domain of human heat shock 70kDa protein 1B. Deposited 2010-02-03 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain E 534–641（108 aa） Fragment：C-terminal domain
Chain F 534–641（108 aa） Fragment：C-terminal domain
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；294 K；2.4 M sodium malonate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Resolution 2.40 Å R-free 0.235
4J8F Crystal structure of a fusion protein containing the NBD of Hsp70 and the middle domain of Hip Deposited 2013-02-14 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–382（382 aa） Fragment：P08107 residues 1-382, P50503 residues 77-247
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 2 MG MAGNESIUM ION × 2 PO4 PHOSPHATE ION × 2 IOD IODIDE ION × 34 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；291 K；17 % PEG-3350 and 0.2 M NH4I, pH 7.4, vapor diffusion, hanging drop, temperature 291K
Resolution 2.70 Å R-free 0.261
4J8F Crystal structure of a fusion protein containing the NBD of Hsp70 and the middle domain of Hip Deposited 2013-02-14 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–382（382 aa） Fragment：P08107 residues 1-382, P50503 residues 77-247
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 PO4 PHOSPHATE ION × 1 IOD IODIDE ION × 17 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；291 K；17 % PEG-3350 and 0.2 M NH4I, pH 7.4, vapor diffusion, hanging drop, temperature 291K
Resolution 2.70 Å R-free 0.261
4PO2 Crystal Structure of the Stress-Inducible Human Heat Shock Protein HSP70 Substrate-Binding Domain in Complex with Peptide Substrate Deposited 2014-02-24 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 386–613（228 aa） Fragment：C-TERMINAL SUBSTRATE-BINDING DOMAIN
Not recorded SO4 SULFATE ION × 1 PO4 PHOSPHATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；293 K；0.1M Bis-Tris (pH 5.5), 0.2M Li2SO4, 28~30% PEG3350 in the reservoir and 0.1M Bis-Tris (pH 5.5), 0.2M Li2SO4, 22~25% PEG3350 in the crystallization drop, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Resolution 2.00 Å R-free 0.222
4PO2 Crystal Structure of the Stress-Inducible Human Heat Shock Protein HSP70 Substrate-Binding Domain in Complex with Peptide Substrate Deposited 2014-02-24 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 386–613（228 aa） Fragment：C-TERMINAL SUBSTRATE-BINDING DOMAIN
Not recorded SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；293 K；0.1M Bis-Tris (pH 5.5), 0.2M Li2SO4, 28~30% PEG3350 in the reservoir and 0.1M Bis-Tris (pH 5.5), 0.2M Li2SO4, 22~25% PEG3350 in the crystallization drop, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Resolution 2.00 Å R-free 0.222
4PO2 Crystal Structure of the Stress-Inducible Human Heat Shock Protein HSP70 Substrate-Binding Domain in Complex with Peptide Substrate Deposited 2014-02-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain A 386–613（228 aa） Fragment：C-TERMINAL SUBSTRATE-BINDING DOMAIN
Chain B 386–613（228 aa） Fragment：C-TERMINAL SUBSTRATE-BINDING DOMAIN
Not recorded SO4 SULFATE ION × 4 PO4 PHOSPHATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；293 K；0.1M Bis-Tris (pH 5.5), 0.2M Li2SO4, 28~30% PEG3350 in the reservoir and 0.1M Bis-Tris (pH 5.5), 0.2M Li2SO4, 22~25% PEG3350 in the crystallization drop, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Resolution 2.00 Å R-free 0.222
4WV5 HEAT SHOCK PROTEIN 70 SUBSTRATE BINDING DOMAIN Deposited 2014-11-04 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 395–543（149 aa） Fragment：unp residues 395-543
Not recorded GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；294 K；11 mg/ml protein in 25mM Tris-HCl, 150 mM NaCl, 1 mM TCEP was mixed 1:1 with reservior solution containing 0.1 M Sodium Acetate, pH 4.5, 2M Ammonium Sulfate
Resolution 2.04 Å R-free 0.224
4WV5 HEAT SHOCK PROTEIN 70 SUBSTRATE BINDING DOMAIN Deposited 2014-11-04 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 395–543（149 aa） Fragment：unp residues 395-543
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；294 K；11 mg/ml protein in 25mM Tris-HCl, 150 mM NaCl, 1 mM TCEP was mixed 1:1 with reservior solution containing 0.1 M Sodium Acetate, pH 4.5, 2M Ammonium Sulfate
Resolution 2.04 Å R-free 0.224
4WV7 HEAT SHOCK PROTEIN 70 SUBSTRATE BINDING DOMAIN WITH COVALENTLY LINKED NOVOLACTONE Deposited 2014-11-04 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 395–543（149 aa） Fragment：unp residues 395-543
Not recorded 3UM (5beta,6alpha,8alpha,14alpha)-13-ethenyl-5,6-dihydroxy-14-methylpodocarp-12-en-15-oic acid × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；294 K；10 mg/ml covalently modified protein in 25 mM Tris-HCl, 50 mM NaCl, 1 mM TCEP was mixed 1:1 with reservior solution containing 0.1 M HEPES, pH 7.0, 70% 2-methyl-2,4-pentanediol
Resolution 2.42 Å R-free 0.272
4WV7 HEAT SHOCK PROTEIN 70 SUBSTRATE BINDING DOMAIN WITH COVALENTLY LINKED NOVOLACTONE Deposited 2014-11-04 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 395–543（149 aa） Fragment：unp residues 395-543
Not recorded 3UM (5beta,6alpha,8alpha,14alpha)-13-ethenyl-5,6-dihydroxy-14-methylpodocarp-12-en-15-oic acid × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；294 K；10 mg/ml covalently modified protein in 25 mM Tris-HCl, 50 mM NaCl, 1 mM TCEP was mixed 1:1 with reservior solution containing 0.1 M HEPES, pH 7.0, 70% 2-methyl-2,4-pentanediol
Resolution 2.42 Å R-free 0.272

15 other PDB entries and 26 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name HSP71_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 5–392； UniProt 1–388

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

SAXS profile for 3atu

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 3atu
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2. Structure Basics 2. Structure Basics

Entry ID entry_id3atu
Deposition date deposition_date2011-01-13
Structure title titleCrystal structure of human Hsp70 NBD in the ADP- and Mg ion-bound state
Keywords keywordsStructural Genomics, RIKEN Structural Genomics/Proteomics Initiative, RSGI, ATPase, ADP binding, Hydrolase; HYDROLASE
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier21.94 Å
Radius of gyration Rg (electron density) rg_electron21.07 Å
Forward intensity I(0) i031057900.00
Molecular weight molecular_weight42370.0 kDa
Excluded volume excluded_volume52846 ų
Envelope volume envelope_volume61821 ų
Hydration-shell volume shell_volume24201 ų
Envelope diameter envelope_diameter73.6 Å
Shell Rg shell_rg28.08 Å
Envelope Rg envelope_rg21.27 Å
Shape Rg shape_rg21.08 Å
Total Rg total_rg21.88 Å
Total atoms total_atoms2980
Residues n_residues379
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax70.8 Å
Rg (real space) rg_real21.82 Å
Rg uncertainty (real space) rg_real_error0.38 Å
I(0) (real space) i0_real3.1060e+07
I(0) uncertainty (real space) i0_real_error4.1350e+05
Rg (reciprocal space) rg_reciprocal21.84 Å
I(0) (reciprocal space) i0_reciprocal31060000.0000
Solution quality estimate total_estimate0.8934
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary26.4 Å
Skewness Skewness skewness0.213
Kurtosis Kurtosis kurtosis-0.400
Angular range angular_range— – 0.3600 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha8443000.0000
Real-space data points n_real_points68
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.872; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.994
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (7)

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7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd3atua1
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.55 — Ribonuclease H-like motif
Superfamily Superfamily superfamilyc.55.1 — Actin-like ATPase domain
Family Family familyc.55.1.1 — Actin/HSP70
Domain ID domain_idd3atua2
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.55 — Ribonuclease H-like motif
Superfamily Superfamily superfamilyc.55.1 — Actin-like ATPase domain
Family Family familyc.55.1.1 — Actin/HSP70

CATH v4.4 (4 domains)

Domain ID domain_id3atuA01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology420 — Nucleotidyltransferase; domain 5
Homologous superfamily homologous superfamily40 — ATPase, nucleotide binding domain
Domain ID domain_id3atuA02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology30 — Defensin A-like
Homologous superfamily homologous superfamily30 —
Domain ID domain_id3atuA03
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology420 — Nucleotidyltransferase; domain 5
Homologous superfamily homologous superfamily40 — ATPase, nucleotide binding domain
Domain ID domain_id3atuA04
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology640 — Actin; Chain A, domain 4
Homologous superfamily homologous superfamily10 — ATPase, substrate binding domain, subdomain 4
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8. Citations (1)

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9. Files and Curves (10)