5aqg

Fragment-based screening of HSP70 sheds light on the functional role of ATP-binding site residues

Method: X-RAY DIFFRACTION Dmax: 174.8 Å Quality: GOOD

1. Protein Identity and Related Structures Protein Identity & Related Structures

HEAT SHOCK COGNATE 71 KDA PROTEIN

HOMO SAPIENS

UniProt P11142

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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain A; UniProt 1–381 Fragment:NUCLEOTIDE BINDING DOMAIN, RESIDUES 1-381 BAG FAMILY MOLECULAR CHAPERONE REGULATOR 1 × 1 (Q99933) ZJB (2R,3R,4S,5R)-2-(3-AMINO-5-METHYL-1,4,5,6,8-PENTAAZAACENAPHTHYLEN-1(5H)-YL)-5-(HYDROXYMETHYL)TETRAHYDROFURAN-3,4-DIOL × 1 GOL GLYCEROL × 2 TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 CL CHLORIDE ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:pH 8.5;16-26% (W/V) PEG3350, 0.1 M K-NA TARTRATE, 0.1 M TRIS.HCL PH 8.5 AND 25% (V/V) GLYCEROL Resolution 2.24 Å R-free 0.222
2 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain C; UniProt 1–381 Fragment:NUCLEOTIDE BINDING DOMAIN, RESIDUES 1-381 BAG FAMILY MOLECULAR CHAPERONE REGULATOR 1 × 1 (Q99933) ZJB (2R,3R,4S,5R)-2-(3-AMINO-5-METHYL-1,4,5,6,8-PENTAAZAACENAPHTHYLEN-1(5H)-YL)-5-(HYDROXYMETHYL)TETRAHYDROFURAN-3,4-DIOL × 1 GOL GLYCEROL × 6 TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 CL CHLORIDE ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:pH 8.5;16-26% (W/V) PEG3350, 0.1 M K-NA TARTRATE, 0.1 M TRIS.HCL PH 8.5 AND 25% (V/V) GLYCEROL Resolution 2.24 Å R-free 0.222
3 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain E; UniProt 1–381 Fragment:NUCLEOTIDE BINDING DOMAIN, RESIDUES 1-381 BAG FAMILY MOLECULAR CHAPERONE REGULATOR 1 × 1 (Q99933) ZJB (2R,3R,4S,5R)-2-(3-AMINO-5-METHYL-1,4,5,6,8-PENTAAZAACENAPHTHYLEN-1(5H)-YL)-5-(HYDROXYMETHYL)TETRAHYDROFURAN-3,4-DIOL × 1 GOL GLYCEROL × 4 X-RAY DIFFRACTION X-ray crystallization conditions:pH 8.5;16-26% (W/V) PEG3350, 0.1 M K-NA TARTRATE, 0.1 M TRIS.HCL PH 8.5 AND 25% (V/V) GLYCEROL Resolution 2.24 Å R-free 0.222

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.

37 other PDB entries and 64 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name HSP7C_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 6–386; UniProt 1–381 Author chain C; PDBConstruct 6–386; UniProt 1–381 Author chain E; PDBConstruct 6–386; UniProt 1–381

BAG FAMILY MOLECULAR CHAPERONE REGULATOR 1

HOMO SAPIENS

UniProt Q99933

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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain B; UniProt 222–334 Fragment:RESIDUES 222-334 HEAT SHOCK COGNATE 71 KDA PROTEIN × 1 (P11142) ZJB (2R,3R,4S,5R)-2-(3-AMINO-5-METHYL-1,4,5,6,8-PENTAAZAACENAPHTHYLEN-1(5H)-YL)-5-(HYDROXYMETHYL)TETRAHYDROFURAN-3,4-DIOL × 1 GOL GLYCEROL × 2 TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 CL CHLORIDE ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:pH 8.5;16-26% (W/V) PEG3350, 0.1 M K-NA TARTRATE, 0.1 M TRIS.HCL PH 8.5 AND 25% (V/V) GLYCEROL Resolution 2.24 Å R-free 0.222
2 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain D; UniProt 222–334 Fragment:RESIDUES 222-334 HEAT SHOCK COGNATE 71 KDA PROTEIN × 1 (P11142) ZJB (2R,3R,4S,5R)-2-(3-AMINO-5-METHYL-1,4,5,6,8-PENTAAZAACENAPHTHYLEN-1(5H)-YL)-5-(HYDROXYMETHYL)TETRAHYDROFURAN-3,4-DIOL × 1 GOL GLYCEROL × 6 TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 CL CHLORIDE ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:pH 8.5;16-26% (W/V) PEG3350, 0.1 M K-NA TARTRATE, 0.1 M TRIS.HCL PH 8.5 AND 25% (V/V) GLYCEROL Resolution 2.24 Å R-free 0.222
3 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain F; UniProt 222–334 Fragment:RESIDUES 222-334 HEAT SHOCK COGNATE 71 KDA PROTEIN × 1 (P11142) ZJB (2R,3R,4S,5R)-2-(3-AMINO-5-METHYL-1,4,5,6,8-PENTAAZAACENAPHTHYLEN-1(5H)-YL)-5-(HYDROXYMETHYL)TETRAHYDROFURAN-3,4-DIOL × 1 GOL GLYCEROL × 4 X-RAY DIFFRACTION X-ray crystallization conditions:pH 8.5;16-26% (W/V) PEG3350, 0.1 M K-NA TARTRATE, 0.1 M TRIS.HCL PH 8.5 AND 25% (V/V) GLYCEROL Resolution 2.24 Å R-free 0.222

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.

28 other PDB entries and 45 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name BAG1_HUMAN
Isoform
PDB entities 2
Chains and sequence ranges Author chain B; PDBConstruct 6–118; UniProt 222–334 Author chain D; PDBConstruct 6–118; UniProt 222–334 Author chain F; PDBConstruct 6–118; UniProt 222–334

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 5aqg

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 5aqg
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2. Structure Basics 2. Structure Basics

Entry ID entry_id5aqg
Deposition date deposition_date2015-09-22
Structure title titleFragment-based screening of HSP70 sheds light on the functional role of ATP-binding site residues
Keywords keywordsHEAT SHOCK PROTEIN, HSP70, HSP72, HSC70, ATPASE, BAG1, CHAPERONE, FRAGMENT; CHAPERONE
Experimental Method methodX-RAY DIFFRACTION

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier50.72
Radius of gyration Rg (electron density) rg_electron51.33
Forward intensity I(0) i0387401000.00
Molecular weight molecular_weight161530.0 kDa
Excluded volume excluded_volume202000 ų
Envelope volume envelope_volume292820 ų
Hydration-shell volume shell_volume52512 ų
Envelope diameter envelope_diameter183.9
Shell Rg shell_rg47.94
Envelope Rg envelope_rg50.08
Shape Rg shape_rg51.36
Total Rg total_rg51.09
Total atoms total_atoms11361
Residues n_residues1481
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 −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

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax174.8
Rg (real space) rg_real51.13
Rg uncertainty (real space) rg_real_error1.96
I(0) (real space) i0_real3.8740e+08
I(0) uncertainty (real space) i0_real_error8.1910e+06
Rg (reciprocal space) rg_reciprocal50.37
I(0) (reciprocal space) i0_reciprocal387000000.0000
Solution quality estimate total_estimate0.7856
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary39.5
Skewness Skewness skewness0.503
Kurtosis Kurtosis kurtosis-0.457
Angular range angular_range— – 0.1550 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha27270000.0000
Real-space data points n_real_points32
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.745; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.588; Smooth: 0.386

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (7)

7. Fold Classification (SCOP + CATH) 21 domains

SCOP 2.08 (6 domains)

Domain ID domain_idd5aqga1
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_idd5aqga2
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_idd5aqgc1
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_idd5aqgc2
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_idd5aqge1
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_idd5aqge2
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 (15 domains)

Domain ID domain_id5aqgA01
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_id5aqgA02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology30 — Defensin A-like
Homologous superfamily homologous superfamily30
Domain ID domain_id5aqgA03
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_id5aqgA04
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
Domain ID domain_id5aqgB00
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology58 — Methane Monooxygenase Hydroxylase; Chain G, domain 1
Homologous superfamily homologous superfamily120 — BAG domain
Domain ID domain_id5aqgC01
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_id5aqgC02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology30 — Defensin A-like
Homologous superfamily homologous superfamily30
Domain ID domain_id5aqgC03
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_id5aqgC04
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
Domain ID domain_id5aqgD00
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology58 — Methane Monooxygenase Hydroxylase; Chain G, domain 1
Homologous superfamily homologous superfamily120 — BAG domain
Domain ID domain_id5aqgE01
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_id5aqgE02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology30 — Defensin A-like
Homologous superfamily homologous superfamily30
Domain ID domain_id5aqgE03
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_id5aqgE04
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
Domain ID domain_id5aqgF00
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology58 — Methane Monooxygenase Hydroxylase; Chain G, domain 1
Homologous superfamily homologous superfamily120 — BAG domain

8. Citations (1)

9. Files and Curves (10)