6th4

Tubulin-inhibitor complex

Method: X-RAY DIFFRACTION Dmax: 175.0 Å Quality: REASONABLE

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

Stathmin-4

Rattus norvegicus

UniProt P63043

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 × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain E; UniProt 75–216 Mutation:C14A, F20W Non-standard monomer:Yes (specific site not provided by mmCIF) Tubulin alpha chain × 2 Tubulin beta chain × 2 SO4 SULFATE ION × 7 GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2 GDP GUANOSINE-5'-DIPHOSPHATE × 2 N9B 1,2,3,9-tetramethoxy-6-methylidene-5~{H}-cyclohepta[a]naphthalen-8-one × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;293 K;PEG, LiSO4, PIPES BUFFER, pH 6.80 Resolution 2.12 Å R-free 0.226

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.

287 other PDB entries and 287 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name STMN4_RAT
Isoform P63043-3
PDB entities 3
Chains and sequence ranges Author chain E; PDBConstruct 2–143; UniProt 75–216

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 6th4

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 6th4
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2. Structure Basics 2. Structure Basics

Entry ID entry_id6th4
Deposition date deposition_date2019-11-18
Structure title titleTubulin-inhibitor complex
Keywords keywordscytoskeleton, cell division, intracellular transport, TRANSPORT PROTEIN, MICROTUBULE, 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_guinier51.49
Radius of gyration Rg (electron density) rg_electron52.37
Forward intensity I(0) i0685482000.00
Molecular weight molecular_weight210000.0 kDa
Excluded volume excluded_volume259610 ų
Envelope volume envelope_volume335310 ų
Hydration-shell volume shell_volume59630 ų
Envelope diameter envelope_diameter188.5
Shell Rg shell_rg47.09
Envelope Rg envelope_rg52.67
Shape Rg shape_rg52.37
Total Rg total_rg52.19
Total atoms total_atoms14719
Residues n_residues1847
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 dmax175.0
Rg (real space) rg_real52.20
Rg uncertainty (real space) rg_real_error1.76
I(0) (real space) i0_real6.8550e+08
I(0) uncertainty (real space) i0_real_error1.4220e+07
Rg (reciprocal space) rg_reciprocal50.89
I(0) (reciprocal space) i0_reciprocal684300000.0000
Solution quality estimate total_estimate0.6725
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary39.5
Skewness Skewness skewness0.665
Kurtosis Kurtosis kurtosis-0.357
Angular range angular_range— – 0.1550 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha196600000.0000
Real-space data points n_real_points32
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.433; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.337; Smooth: 0.102

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (9)

7. Fold Classification (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

Domain ID domain_id6th4A01
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_id6th4A02
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_id6th4B01
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_id6th4B02
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_id6th4C01
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_id6th4C02
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_id6th4D01
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_id6th4D02
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

8. Citations (1)

9. Files and Curves (10)