5uci

Hsp90b N-terminal domain with inhibitors

Method: X-RAY DIFFRACTION Dmax: 99.8 Å Quality: EXCELLENT

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

Heat shock protein HSP 90-beta

Homo sapiens

UniProt P08238

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 1–218 Fragment:UNP residues 1-218 874 (2,4-Dihydroxy-3-(hydroxymethyl)-5-isopropylphenyl)(isoindolin-2-yl)methanone × 1 DMS DIMETHYL SULFOXIDE × 1 X-RAY DIFFRACTION X-ray crystallization conditions:EVAPORATION;293 K;30% PEG 8,000, 0.2 M sodium acetate, 0.1 sodium cacodylate pH 6.5 Resolution 2.70 Å R-free 0.238
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain B; UniProt 1–218 Fragment:UNP residues 1-218 874 (2,4-Dihydroxy-3-(hydroxymethyl)-5-isopropylphenyl)(isoindolin-2-yl)methanone × 1 DMS DIMETHYL SULFOXIDE × 1 GOL GLYCEROL × 1 X-RAY DIFFRACTION X-ray crystallization conditions:EVAPORATION;293 K;30% PEG 8,000, 0.2 M sodium acetate, 0.1 sodium cacodylate pH 6.5 Resolution 2.70 Å R-free 0.238
3 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain C; UniProt 1–218 Fragment:UNP residues 1-218 874 (2,4-Dihydroxy-3-(hydroxymethyl)-5-isopropylphenyl)(isoindolin-2-yl)methanone × 1 DMS DIMETHYL SULFOXIDE × 1 X-RAY DIFFRACTION X-ray crystallization conditions:EVAPORATION;293 K;30% PEG 8,000, 0.2 M sodium acetate, 0.1 sodium cacodylate pH 6.5 Resolution 2.70 Å R-free 0.238
4 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain D; UniProt 1–218 Fragment:UNP residues 1-218 874 (2,4-Dihydroxy-3-(hydroxymethyl)-5-isopropylphenyl)(isoindolin-2-yl)methanone × 1 DMS DIMETHYL SULFOXIDE × 1 GOL GLYCEROL × 1 X-RAY DIFFRACTION X-ray crystallization conditions:EVAPORATION;293 K;30% PEG 8,000, 0.2 M sodium acetate, 0.1 sodium cacodylate pH 6.5 Resolution 2.70 Å R-free 0.238

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.

29 other PDB entries and 47 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name HS90B_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 3–220; UniProt 1–218 Author chain B; PDBConstruct 3–220; UniProt 1–218 Author chain C; PDBConstruct 3–220; UniProt 1–218 Author chain D; PDBConstruct 3–220; UniProt 1–218

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 5uci

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id5uci
Deposition date deposition_date2016-12-22
Structure title titleHsp90b N-terminal domain with inhibitors
Keywords keywordsHsp90 inhibitor, Chaperone-Inhibitor complex; Chaperone/Inhibitor
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier32.70
Radius of gyration Rg (electron density) rg_electron31.70
Forward intensity I(0) i0141695000.00
Molecular weight molecular_weight96729.0 kDa
Excluded volume excluded_volume122010 ų
Envelope volume envelope_volume160010 ų
Hydration-shell volume shell_volume41623 ų
Envelope diameter envelope_diameter108.0
Shell Rg shell_rg39.01
Envelope Rg envelope_rg31.37
Shape Rg shape_rg31.70
Total Rg total_rg32.36
Total atoms total_atoms6817
Residues n_residues851
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 dmax99.8
Rg (real space) rg_real32.49
Rg uncertainty (real space) rg_real_error0.64
I(0) (real space) i0_real1.4170e+08
I(0) uncertainty (real space) i0_real_error1.9680e+06
Rg (reciprocal space) rg_reciprocal32.58
I(0) (reciprocal space) i0_reciprocal141700000.0000
Solution quality estimate total_estimate0.9028
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary47.8
Skewness Skewness skewness0.077
Kurtosis Kurtosis kurtosis-0.587
Angular range angular_range— – 0.2400 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha39010000.0000
Real-space data points n_real_points49
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.946; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.994; Smooth: 0.902

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (5)

7. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (6 domains)

Domain ID domain_idd5ucia1
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.122 — ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase
Superfamily Superfamily superfamilyd.122.1 — ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase
Family Family familyd.122.1.1 — Heat shock protein 90, HSP90, N-terminal domain
Domain ID domain_idd5ucia2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd5ucib_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.122 — ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase
Superfamily Superfamily superfamilyd.122.1 — ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase
Family Family familyd.122.1.1 — Heat shock protein 90, HSP90, N-terminal domain
Domain ID domain_idd5ucic1
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.122 — ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase
Superfamily Superfamily superfamilyd.122.1 — ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase
Family Family familyd.122.1.1 — Heat shock protein 90, HSP90, N-terminal domain
Domain ID domain_idd5ucic2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd5ucid_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.122 — ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase
Superfamily Superfamily superfamilyd.122.1 — ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase
Family Family familyd.122.1.1 — Heat shock protein 90, HSP90, N-terminal domain

CATH v4.4 (4 domains)

Domain ID domain_id5uciA00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology565 — Heat Shock Protein 90
Homologous superfamily homologous superfamily10 — Histidine kinase-like ATPase, C-terminal domain
Domain ID domain_id5uciB00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology565 — Heat Shock Protein 90
Homologous superfamily homologous superfamily10 — Histidine kinase-like ATPase, C-terminal domain
Domain ID domain_id5uciC00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology565 — Heat Shock Protein 90
Homologous superfamily homologous superfamily10 — Histidine kinase-like ATPase, C-terminal domain
Domain ID domain_id5uciD00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology565 — Heat Shock Protein 90
Homologous superfamily homologous superfamily10 — Histidine kinase-like ATPase, C-terminal domain

8. Citations (1)

9. Files and Curves (10)