7cpd

Crystal structure of T2R-TTL-(+)-6-Br-JP18 complex

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 (Q9H169) Tubulin tyrosine ligase × 1 (E1BQ43) GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 3 CA CALCIUM ION × 3 G9U (6R)-6-[(6-bromanyl-1H-indol-3-yl)methyl]-6,7,8,9-tetrahydrobenzo[7]annulen-5-one × 2 GDP GUANOSINE-5'-DIPHOSPHATE × 2 MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 GOL GLYCEROL × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 6.7;289 K;6-10% PEG 4k, 4-10% glycerol, 30 mM MgCl2, 100 mM MES/Imidazole pH 6.5-6.9 Resolution 2.51 Å R-free 0.240

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 (Q9H169) Tubulin tyrosine ligase × 1 (E1BQ43) GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 3 CA CALCIUM ION × 3 G9U (6R)-6-[(6-bromanyl-1H-indol-3-yl)methyl]-6,7,8,9-tetrahydrobenzo[7]annulen-5-one × 2 GDP GUANOSINE-5'-DIPHOSPHATE × 2 MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 GOL GLYCEROL × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 6.7;289 K;6-10% PEG 4k, 4-10% glycerol, 30 mM MgCl2, 100 mM MES/Imidazole pH 6.5-6.9 Resolution 2.51 Å R-free 0.240

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

Homo sapiens

UniProt Q9H169

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 1–189 Not recorded Tubulin alpha-1B chain × 2 (P81947) Tubulin beta-2B chain × 2 (Q6B856) Tubulin tyrosine ligase × 1 (E1BQ43) GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 3 CA CALCIUM ION × 3 G9U (6R)-6-[(6-bromanyl-1H-indol-3-yl)methyl]-6,7,8,9-tetrahydrobenzo[7]annulen-5-one × 2 GDP GUANOSINE-5'-DIPHOSPHATE × 2 MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 GOL GLYCEROL × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 6.7;289 K;6-10% PEG 4k, 4-10% glycerol, 30 mM MgCl2, 100 mM MES/Imidazole pH 6.5-6.9 Resolution 2.51 Å R-free 0.240

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.

9 other PDB entries and 9 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name STMN4_HUMAN
Isoform
PDB entities 3
Chains and sequence ranges Author chain E; PDBConstruct 1–189; UniProt 1–189

Tubulin tyrosine ligase

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 (Q9H169) GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 3 CA CALCIUM ION × 3 G9U (6R)-6-[(6-bromanyl-1H-indol-3-yl)methyl]-6,7,8,9-tetrahydrobenzo[7]annulen-5-one × 2 GDP GUANOSINE-5'-DIPHOSPHATE × 2 MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 GOL GLYCEROL × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 6.7;289 K;6-10% PEG 4k, 4-10% glycerol, 30 mM MgCl2, 100 mM MES/Imidazole pH 6.5-6.9 Resolution 2.51 Å R-free 0.240

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 7cpd

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id7cpd
Deposition date deposition_date2020-08-06
Structure title titleCrystal structure of T2R-TTL-(+)-6-Br-JP18 complex
Keywords keywordsCELL CYCLE-INHIBITOR complex; CEll CYCLE/INHIBITOR
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier55.00
Radius of gyration Rg (electron density) rg_electron56.02
Forward intensity I(0) i0867770000.00
Molecular weight molecular_weight241150.0 kDa
Excluded volume excluded_volume299660 ų
Envelope volume envelope_volume402510 ų
Hydration-shell volume shell_volume65517 ų
Envelope diameter envelope_diameter193.5
Shell Rg shell_rg50.13
Envelope Rg envelope_rg56.44
Shape Rg shape_rg56.03
Total Rg total_rg55.80
Total atoms total_atoms17020
Residues n_residues2116
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_real55.72
Rg uncertainty (real space) rg_real_error2.12
I(0) (real space) i0_real8.6780e+08
I(0) uncertainty (real space) i0_real_error1.7790e+07
Rg (reciprocal space) rg_reciprocal54.36
I(0) (reciprocal space) i0_reciprocal866000000.0000
Solution quality estimate total_estimate0.7291
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary37.0
Skewness Skewness skewness0.573
Kurtosis Kurtosis kurtosis-0.536
Angular range angular_range— – 0.1450 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha113100000.0000
Real-space data points n_real_points30
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.599; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.665; Smooth: 0.014

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (12)

7. Fold Classification (SCOP + CATH) 10 domains

CATH v4.4 (10 domains)

Domain ID domain_id7cpdA01
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_id7cpdA02
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_id7cpdB01
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_id7cpdB02
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_id7cpdB03
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology287 — Helix Hairpins
Homologous superfamily homologous superfamily600 — Helix hairpin bin
Domain ID domain_id7cpdC01
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_id7cpdC02
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_id7cpdD01
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_id7cpdD02
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_id7cpdF01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily11480

8. Citations (1)

9. Files and Curves (10)