5o7a

Quinolin-6-yloxyacetamides are microtubule destabilizing agents that bind to the colchicine site of tubulin

Method: X-RAY DIFFRACTION Dmax: 178.7 Å Quality: REASONABLE

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 × 6 PDB declaration: hexameric(6) Consistent with protein copy count Chain A; UniProt 1–451 Chain C; UniProt 1–451 Not recorded Tubulin beta-2B chain × 2 (Q6B856) Stathmin-4 × 1 (P63043) Uncharacterized protein × 1 (E1BQ43) GTP GUANOSINE-5'-TRIPHOSPHATE × 2 GDP GUANOSINE-5'-DIPHOSPHATE × 2 MG MAGNESIUM ION × 4 9N5 (2~{R})-2-(3-ethynylquinolin-6-yl)oxy-2-methoxy-~{N}-[(1~{E})-1-methoxyimino-2-methyl-propan-2-yl]ethanamide × 2 ACP PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 6.7;293 K;10% PEG 4000, 20% glycerol, 30 mM CaCl2, 30 mM MgCl2, 0.1 M MES/imidazole, pH 6.7, 1 mM AMPPCP, 10 mM DTT, 0.1 mM GDP Resolution 2.50 Å R-free 0.256

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 1–451; UniProt 1–451 Author chain C; PDBConstruct 1–451; UniProt 1–451

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 × 6 PDB declaration: hexameric(6) Consistent with protein copy count Chain B; UniProt 1–445 Chain D; UniProt 1–445 Not recorded Tubulin alpha-1B chain × 2 (P81947) Stathmin-4 × 1 (P63043) Uncharacterized protein × 1 (E1BQ43) GTP GUANOSINE-5'-TRIPHOSPHATE × 2 GDP GUANOSINE-5'-DIPHOSPHATE × 2 MG MAGNESIUM ION × 4 9N5 (2~{R})-2-(3-ethynylquinolin-6-yl)oxy-2-methoxy-~{N}-[(1~{E})-1-methoxyimino-2-methyl-propan-2-yl]ethanamide × 2 ACP PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 6.7;293 K;10% PEG 4000, 20% glycerol, 30 mM CaCl2, 30 mM MgCl2, 0.1 M MES/imidazole, pH 6.7, 1 mM AMPPCP, 10 mM DTT, 0.1 mM GDP Resolution 2.50 Å R-free 0.256

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 1–445; UniProt 1–445 Author chain D; PDBConstruct 1–445; UniProt 1–445

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 × 6 PDB declaration: hexameric(6) Consistent with protein copy count Chain E; UniProt 49–189 Not recorded Tubulin alpha-1B chain × 2 (P81947) Tubulin beta-2B chain × 2 (Q6B856) Uncharacterized protein × 1 (E1BQ43) GTP GUANOSINE-5'-TRIPHOSPHATE × 2 GDP GUANOSINE-5'-DIPHOSPHATE × 2 MG MAGNESIUM ION × 4 9N5 (2~{R})-2-(3-ethynylquinolin-6-yl)oxy-2-methoxy-~{N}-[(1~{E})-1-methoxyimino-2-methyl-propan-2-yl]ethanamide × 2 ACP PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 6.7;293 K;10% PEG 4000, 20% glycerol, 30 mM CaCl2, 30 mM MgCl2, 0.1 M MES/imidazole, pH 6.7, 1 mM AMPPCP, 10 mM DTT, 0.1 mM GDP Resolution 2.50 Å R-free 0.256

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
PDB entities 3
Chains and sequence ranges Author chain E; PDBConstruct 3–143; UniProt 49–189

Uncharacterized protein

Gallus gallus

UniProt E1BQ43

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 × 6 PDB declaration: hexameric(6) Consistent with protein copy count Chain F; UniProt 1–378 Not recorded Tubulin alpha-1B chain × 2 (P81947) Tubulin beta-2B chain × 2 (Q6B856) Stathmin-4 × 1 (P63043) GTP GUANOSINE-5'-TRIPHOSPHATE × 2 GDP GUANOSINE-5'-DIPHOSPHATE × 2 MG MAGNESIUM ION × 4 9N5 (2~{R})-2-(3-ethynylquinolin-6-yl)oxy-2-methoxy-~{N}-[(1~{E})-1-methoxyimino-2-methyl-propan-2-yl]ethanamide × 2 ACP PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 6.7;293 K;10% PEG 4000, 20% glycerol, 30 mM CaCl2, 30 mM MgCl2, 0.1 M MES/imidazole, pH 6.7, 1 mM AMPPCP, 10 mM DTT, 0.1 mM GDP Resolution 2.50 Å R-free 0.256

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.

241 other PDB entries and 241 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name E1BQ43_CHICK
Isoform
PDB entities 4
Chains and sequence ranges Author chain F; PDBConstruct 1–378; UniProt 1–378

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 5o7a

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 5o7a
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2. Structure Basics 2. Structure Basics

Entry ID entry_id5o7a
Deposition date deposition_date2017-06-08
Structure title titleQuinolin-6-yloxyacetamides are microtubule destabilizing agents that bind to the colchicine site of tubulin
Keywords keywordsMicrotubules, Tubulin, Colchicine, Quinolin-6-yloxyacetamides, motor protein; MOTOR PROTEIN
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier54.48
Radius of gyration Rg (electron density) rg_electron55.52
Forward intensity I(0) i0853107000.00
Molecular weight molecular_weight238590.0 kDa
Excluded volume excluded_volume296420 ų
Envelope volume envelope_volume389170 ų
Hydration-shell volume shell_volume64550 ų
Envelope diameter envelope_diameter192.7
Shell Rg shell_rg49.40
Envelope Rg envelope_rg55.62
Shape Rg shape_rg55.51
Total Rg total_rg55.35
Total atoms total_atoms16846
Residues n_residues2089
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 dmax178.7
Rg (real space) rg_real55.18
Rg uncertainty (real space) rg_real_error2.06
I(0) (real space) i0_real8.5310e+08
I(0) uncertainty (real space) i0_real_error1.8000e+07
Rg (reciprocal space) rg_reciprocal53.88
I(0) (reciprocal space) i0_reciprocal851500000.0000
Solution quality estimate total_estimate0.7299
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary37.0
Skewness Skewness skewness0.575
Kurtosis Kurtosis kurtosis-0.529
Angular range angular_range— – 0.1450 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha102300000.0000
Real-space data points n_real_points30
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.600; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.667; Smooth: 0.017

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (10)

7. Fold Classification (SCOP + CATH) 26 domains

SCOP 2.08 (11 domains)

Domain ID domain_idd5o7aa1
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.32 — Tubulin nucleotide-binding domain-like
Superfamily Superfamily superfamilyc.32.1 — Tubulin nucleotide-binding domain-like
Family Family familyc.32.1.1 — Tubulin, GTPase domain
Domain ID domain_idd5o7aa2
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.79 — Bacillus chorismate mutase-like
Superfamily Superfamily superfamilyd.79.2 — Tubulin C-terminal domain-like
Family Family familyd.79.2.1 — Tubulin, C-terminal domain
Domain ID domain_idd5o7ab1
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.32 — Tubulin nucleotide-binding domain-like
Superfamily Superfamily superfamilyc.32.1 — Tubulin nucleotide-binding domain-like
Family Family familyc.32.1.1 — Tubulin, GTPase domain
Domain ID domain_idd5o7ab2
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.79 — Bacillus chorismate mutase-like
Superfamily Superfamily superfamilyd.79.2 — Tubulin C-terminal domain-like
Family Family familyd.79.2.1 — Tubulin, C-terminal domain
Domain ID domain_idd5o7ac1
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.32 — Tubulin nucleotide-binding domain-like
Superfamily Superfamily superfamilyc.32.1 — Tubulin nucleotide-binding domain-like
Family Family familyc.32.1.1 — Tubulin, GTPase domain
Domain ID domain_idd5o7ac2
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.79 — Bacillus chorismate mutase-like
Superfamily Superfamily superfamilyd.79.2 — Tubulin C-terminal domain-like
Family Family familyd.79.2.1 — Tubulin, C-terminal domain
Domain ID domain_idd5o7ad1
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.32 — Tubulin nucleotide-binding domain-like
Superfamily Superfamily superfamilyc.32.1 — Tubulin nucleotide-binding domain-like
Family Family familyc.32.1.1 — Tubulin, GTPase domain
Domain ID domain_idd5o7ad2
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.79 — Bacillus chorismate mutase-like
Superfamily Superfamily superfamilyd.79.2 — Tubulin C-terminal domain-like
Family Family familyd.79.2.1 — Tubulin, C-terminal domain
Domain ID domain_idd5o7ae_
Class classa — All alpha proteins
Fold Fold folda.137 — Non-globular all-alpha subunits of globular proteins
Superfamily Superfamily superfamilya.137.10 — Stathmin
Family Family familya.137.10.1 — Stathmin
Domain ID domain_idd5o7af1
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.30 — PreATP-grasp domain
Superfamily Superfamily superfamilyc.30.1 — PreATP-grasp domain
Family Family familyc.30.1.9 — Tubulin tyrosine ligase (TTL) N-terminal domain-like
Domain ID domain_idd5o7af2
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.142 — ATP-grasp
Superfamily Superfamily superfamilyd.142.1 — Glutathione synthetase ATP-binding domain-like
Family Family familyd.142.1.10 — Tubulin tyrosine ligase (TTL) C-terminal domain-like

CATH v4.4 (15 domains)

Domain ID domain_id5o7aA01
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_id5o7aA02
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_id5o7aA03
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology287 — Helix Hairpins
Homologous superfamily homologous superfamily600 — Helix hairpin bin
Domain ID domain_id5o7aB01
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_id5o7aB02
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_id5o7aB03
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology287 — Helix Hairpins
Homologous superfamily homologous superfamily600 — Helix hairpin bin
Domain ID domain_id5o7aC01
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_id5o7aC02
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_id5o7aC03
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology287 — Helix Hairpins
Homologous superfamily homologous superfamily600 — Helix hairpin bin
Domain ID domain_id5o7aD01
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_id5o7aD02
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_id5o7aD03
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology287 — Helix Hairpins
Homologous superfamily homologous superfamily600 — Helix hairpin bin
Domain ID domain_id5o7aE01
Class class6 — Special
Architecture architecture10 — Helix non-globular
Topology topology280 — Methane Monooxygenase Hydroxylase; Chain G, domain 1
Homologous superfamily homologous superfamily30
Domain ID domain_id5o7aF01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily11480
Domain ID domain_id5o7aF02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology470 — D-amino Acid Aminotransferase; Chain A, domain 1
Homologous superfamily homologous superfamily20 — ATP-grasp fold, B domain

8. Citations (1)

9. Files and Curves (10)