7pjf

Inhibiting parasite proliferation using a rationally designed anti-tubulin agent

Method: X-RAY DIFFRACTION Dmax: 121.0 Å Quality: REASONABLE

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

Tubulin alpha-1B chain

Homo sapiens

UniProt P68363

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 1–451 Not recorded Tubulin beta-3 chain × 1 (Q13509) Designed ankyrin repeat protein (DARPIN) D1 × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION;pH 5.5;293 K;100 mM Bis-TrisMethane, pH 5.5, supplemented with 200 mM ammonium sulfate and 25% PEG3350 Resolution 1.86 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.

38 other PDB entries and 38 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name TBA1B_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–451; UniProt 1–451

Tubulin beta-3 chain

Homo sapiens

UniProt Q13509

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 1–450 Not recorded Tubulin alpha-1B chain × 1 (P68363) Designed ankyrin repeat protein (DARPIN) D1 × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION;pH 5.5;293 K;100 mM Bis-TrisMethane, pH 5.5, supplemented with 200 mM ammonium sulfate and 25% PEG3350 Resolution 1.86 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.

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

View Construct and Data Evidence
UniProt name TBB3_HUMAN
Isoform
PDB entities 2
Chains and sequence ranges Author chain B; PDBConstruct 1–450; UniProt 1–450

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 7pjf

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 7pjf
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2. Structure Basics 2. Structure Basics

Entry ID entry_id7pjf
Deposition date deposition_date2021-08-24
Structure title titleInhibiting parasite proliferation using a rationally designed anti-tubulin agent
Keywords keywordsTubulin, Microtubules, Protozoa, Apicomplexa, STRUCTURAL PROTEIN; STRUCTURAL PROTEIN
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier33.89
Radius of gyration Rg (electron density) rg_electron33.93
Forward intensity I(0) i0198813000.00
Molecular weight molecular_weight111020.0 kDa
Excluded volume excluded_volume137750 ų
Envelope volume envelope_volume166820 ų
Hydration-shell volume shell_volume42612 ų
Envelope diameter envelope_diameter131.8
Shell Rg shell_rg38.91
Envelope Rg envelope_rg34.34
Shape Rg shape_rg33.94
Total Rg total_rg34.25
Total atoms total_atoms7794
Residues n_residues1002
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 dmax121.0
Rg (real space) rg_real34.14
Rg uncertainty (real space) rg_real_error1.44
I(0) (real space) i0_real1.9880e+08
I(0) uncertainty (real space) i0_real_error3.9050e+06
Rg (reciprocal space) rg_reciprocal33.98
I(0) (reciprocal space) i0_reciprocal198800000.0000
Solution quality estimate total_estimate0.7455
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary33.5
Skewness Skewness skewness0.625
Kurtosis Kurtosis kurtosis0.027
Angular range angular_range— – 0.2350 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha47860000.0000
Real-space data points n_real_points48
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.644; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.759; Smooth: 0.000

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (6)

7. Fold Classification (SCOP + CATH) 5 domains

CATH v4.4 (5 domains)

Domain ID domain_id7pjfA01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily1440 — Tubulin/FtsZ, GTPase domain
Domain ID domain_id7pjfA02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology1330 — 60s Ribosomal Protein L30; Chain: A;
Homologous superfamily homologous superfamily20 — Tubulin/FtsZ, C-terminal domain
Domain ID domain_id7pjfB01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily1440 — Tubulin/FtsZ, GTPase domain
Domain ID domain_id7pjfB02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology1330 — 60s Ribosomal Protein L30; Chain: A;
Homologous superfamily homologous superfamily20 — Tubulin/FtsZ, C-terminal domain
Domain ID domain_id7pjfB03
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology287 — Helix Hairpins
Homologous superfamily homologous superfamily600 — Helix hairpin bin

8. Citations (1)

9. Files and Curves (10)