8cla

Z-SBTubA4 photoswitch bound to tubulin-DARPin D1 complex

Method: X-RAY DIFFRACTION Dmax: 120.9 Å Quality: GOOD

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

Tubulin alpha-1B chain

OrganismNot specified

UniProt P81947

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 × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain A; UniProt 2–436 Not recorded Tubulin beta-2B chain × 1 (Q6B856) Designed Ankyrin Repeat Protein (DARPIN) D1 × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 CA CALCIUM ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 I8R 2-methoxy-5-[2-(5,6,7-trimethoxy-1,3-benzothiazol-2-yl)ethyl]phenol × 1 X-RAY DIFFRACTION X-ray crystallization conditions:BATCH MODE;pH 5.5;293 K;21% PEG3000 (w/v), 0.2M ammonium sulfate, 0.1M bis-tris methane Resolution 2.00 Å R-free 0.206

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.

249 other PDB entries and 251 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name TBA1B_BOVIN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–435; UniProt 2–436

Tubulin beta-2B chain

OrganismNot specified

UniProt Q6B856

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 × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain B; UniProt 1–431 Not recorded Tubulin alpha-1B chain × 1 (P81947) Designed Ankyrin Repeat Protein (DARPIN) D1 × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 CA CALCIUM ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 I8R 2-methoxy-5-[2-(5,6,7-trimethoxy-1,3-benzothiazol-2-yl)ethyl]phenol × 1 X-RAY DIFFRACTION X-ray crystallization conditions:BATCH MODE;pH 5.5;293 K;21% PEG3000 (w/v), 0.2M ammonium sulfate, 0.1M bis-tris methane Resolution 2.00 Å R-free 0.206

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.

273 other PDB entries and 275 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name TBB2B_BOVIN
Isoform
PDB entities 2
Chains and sequence ranges Author chain B; PDBConstruct 1–430; UniProt 1–431

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 8cla

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 8cla
Download Download

2. Structure Basics 2. Structure Basics

Entry ID entry_id8cla
Deposition date deposition_date2023-02-16
最后修订 last_revision2024-02-28
Structure title titleZ-SBTubA4 photoswitch bound to tubulin-DARPin D1 complex
Keywords keywordsDrug-tubulin-complex Cell cycle inhibition, CELL CYCLE; CELL CYCLE
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier33.86
Radius of gyration Rg (electron density) rg_electron33.89
Forward intensity I(0) i0207654000.00
Molecular weight molecular_weight113500.0 kDa
Excluded volume excluded_volume140710 ų
Envelope volume envelope_volume166000 ų
Hydration-shell volume shell_volume42385 ų
Envelope diameter envelope_diameter133.4
Shell Rg shell_rg38.99
Envelope Rg envelope_rg34.42
Shape Rg shape_rg33.89
Total Rg total_rg34.22
Total atoms total_atoms15625
Residues n_residues1020
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 dmax120.9
Rg (real space) rg_real34.12
Rg uncertainty (real space) rg_real_error1.27
I(0) (real space) i0_real2.0770e+08
I(0) uncertainty (real space) i0_real_error3.9920e+06
Rg (reciprocal space) rg_reciprocal33.96
I(0) (reciprocal space) i0_reciprocal207600000.0000
Solution quality estimate total_estimate0.8095
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary33.5
Skewness Skewness skewness0.631
Kurtosis Kurtosis kurtosis0.037
Angular range angular_range— – 0.2350 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha44310000.0000
Real-space data points n_real_points48
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.649; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.748; Smooth: 0.824

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (9)

8. Citations (1)

9. Files and Curves (10)