8ahm

Crystal structure of tubulin in complex with C(13)/C(13')-Bis-Desmethyl-Disorazole Z

Method: X-RAY DIFFRACTION Dmax: 186.6 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) Tubulin tyrosine ligase × 1 (E1BQ43) GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 5 GOL GLYCEROL × 1 CA CALCIUM ION × 4 DMS DIMETHYL SULFOXIDE × 2 GDP GUANOSINE-5'-DIPHOSPHATE × 2 MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 2 M5U dimethyl 2,2'-((12Z,122Z,4S,6Z,8E,10E,15S,17Z,19E,21E)-2,13-dioxo-3,14-dioxa-1(4,2),12(2,4)-dioxazolacyclodocosaphane-6,8,10,17,19,21-hexaene-4,15-diyl)(2S,2'S,3S,3'S,4E,4'E)-bis(3-hydroxyhex-4-enoate) × 1 ACP PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6.5;293.15 K;0.1 M MES/0.1 M Imidazole pH 6.5, 0.03 M CaCl2/ MgCl2, 5 mM L-Tyr, 8% glycerol, 5.5 % PEG 4000 Resolution 2.42 Å R-free 0.241

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) Tubulin tyrosine ligase × 1 (E1BQ43) GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 5 GOL GLYCEROL × 1 CA CALCIUM ION × 4 DMS DIMETHYL SULFOXIDE × 2 GDP GUANOSINE-5'-DIPHOSPHATE × 2 MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 2 M5U dimethyl 2,2'-((12Z,122Z,4S,6Z,8E,10E,15S,17Z,19E,21E)-2,13-dioxo-3,14-dioxa-1(4,2),12(2,4)-dioxazolacyclodocosaphane-6,8,10,17,19,21-hexaene-4,15-diyl)(2S,2'S,3S,3'S,4E,4'E)-bis(3-hydroxyhex-4-enoate) × 1 ACP PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6.5;293.15 K;0.1 M MES/0.1 M Imidazole pH 6.5, 0.03 M CaCl2/ MgCl2, 5 mM L-Tyr, 8% glycerol, 5.5 % PEG 4000 Resolution 2.42 Å R-free 0.241

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 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 × 5 GOL GLYCEROL × 1 CA CALCIUM ION × 4 DMS DIMETHYL SULFOXIDE × 2 GDP GUANOSINE-5'-DIPHOSPHATE × 2 MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 2 M5U dimethyl 2,2'-((12Z,122Z,4S,6Z,8E,10E,15S,17Z,19E,21E)-2,13-dioxo-3,14-dioxa-1(4,2),12(2,4)-dioxazolacyclodocosaphane-6,8,10,17,19,21-hexaene-4,15-diyl)(2S,2'S,3S,3'S,4E,4'E)-bis(3-hydroxyhex-4-enoate) × 1 ACP PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6.5;293.15 K;0.1 M MES/0.1 M Imidazole pH 6.5, 0.03 M CaCl2/ MgCl2, 5 mM L-Tyr, 8% glycerol, 5.5 % PEG 4000 Resolution 2.42 Å R-free 0.241

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 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 (P63043) GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 5 GOL GLYCEROL × 1 CA CALCIUM ION × 4 DMS DIMETHYL SULFOXIDE × 2 GDP GUANOSINE-5'-DIPHOSPHATE × 2 MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 2 M5U dimethyl 2,2'-((12Z,122Z,4S,6Z,8E,10E,15S,17Z,19E,21E)-2,13-dioxo-3,14-dioxa-1(4,2),12(2,4)-dioxazolacyclodocosaphane-6,8,10,17,19,21-hexaene-4,15-diyl)(2S,2'S,3S,3'S,4E,4'E)-bis(3-hydroxyhex-4-enoate) × 1 ACP PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6.5;293.15 K;0.1 M MES/0.1 M Imidazole pH 6.5, 0.03 M CaCl2/ MgCl2, 5 mM L-Tyr, 8% glycerol, 5.5 % PEG 4000 Resolution 2.42 Å R-free 0.241

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 8ahm

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 8ahm
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2. Structure Basics 2. Structure Basics

Entry ID entry_id8ahm
Deposition date deposition_date2022-07-22
Structure title titleCrystal structure of tubulin in complex with C(13)/C(13')-Bis-Desmethyl-Disorazole Z
Keywords keywordstubulin, inhibitor, complex, 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_guinier55.67
Radius of gyration Rg (electron density) rg_electron56.71
Forward intensity I(0) i0914924000.00
Molecular weight molecular_weight247090.0 kDa
Excluded volume excluded_volume306820 ų
Envelope volume envelope_volume408630 ų
Hydration-shell volume shell_volume65865 ų
Envelope diameter envelope_diameter194.5
Shell Rg shell_rg50.33
Envelope Rg envelope_rg56.96
Shape Rg shape_rg56.73
Total Rg total_rg56.45
Total atoms total_atoms34131
Residues n_residues2158
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 dmax186.6
Rg (real space) rg_real56.40
Rg uncertainty (real space) rg_real_error2.11
I(0) (real space) i0_real9.1490e+08
I(0) uncertainty (real space) i0_real_error1.8340e+07
Rg (reciprocal space) rg_reciprocal55.03
I(0) (reciprocal space) i0_reciprocal913000000.0000
Solution quality estimate total_estimate0.7153
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary40.0
Skewness Skewness skewness0.558
Kurtosis Kurtosis kurtosis-0.558
Angular range angular_range— – 0.1400 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha84520000.0000
Real-space data points n_real_points29
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.572; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.555; Smooth: 0.023

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (14)

7. Fold Classification (SCOP + CATH) 11 domains

CATH v4.4 (11 domains)

Domain ID domain_id8ahmA01
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_id8ahmA02
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_id8ahmB01
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_id8ahmB02
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_id8ahmB03
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology287 — Helix Hairpins
Homologous superfamily homologous superfamily600 — Helix hairpin bin
Domain ID domain_id8ahmC01
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_id8ahmC02
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_id8ahmD01
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_id8ahmD02
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_id8ahmF01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily11480
Domain ID domain_id8ahmF02
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)