6o5n

Tubulin-RB3_SLD-TTL in complex with compound 10ab

Method: X-RAY DIFFRACTION

▼

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

Tubulin alpha-1B chain

OrganismNot specified

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 6	Tubulin beta-2B chain × 2 （A0A287AGU7） Stathmin-4 × 1 （Q9H169） Tubulin Tyrosine Ligase × 1 （E1BQ43） GUANOSINE-5'-TRIPHOSPHATE × 2 MAGNESIUM ION × 3 CALCIUM ION × 2 GUANOSINE-5'-DIPHOSPHATE × 2 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 2 [2-(4-methyl-1H-indol-3-yl)-1H-imidazol-5-yl](3,4,5-trimethoxyphenyl)methanone × 2 water × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	TBA1B_PIG
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–450； UniProt 1–450 Author chain C； PDBConstruct 1–450； UniProt 1–450

Tubulin beta-2B chain

OrganismNot specified

UniProt A0A287AGU7

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 6	Tubulin alpha-1B chain × 2 （Q2XVP4） Stathmin-4 × 1 （Q9H169） Tubulin Tyrosine Ligase × 1 （E1BQ43） GUANOSINE-5'-TRIPHOSPHATE × 2 MAGNESIUM ION × 3 CALCIUM ION × 2 GUANOSINE-5'-DIPHOSPHATE × 2 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 2 [2-(4-methyl-1H-indol-3-yl)-1H-imidazol-5-yl](3,4,5-trimethoxyphenyl)methanone × 2 water × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A0A287AGU7_PIG
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	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 6	Tubulin alpha-1B chain × 2 （Q2XVP4） Tubulin beta-2B chain × 2 （A0A287AGU7） Tubulin Tyrosine Ligase × 1 （E1BQ43） GUANOSINE-5'-TRIPHOSPHATE × 2 MAGNESIUM ION × 3 CALCIUM ION × 2 GUANOSINE-5'-DIPHOSPHATE × 2 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 2 [2-(4-methyl-1H-indol-3-yl)-1H-imidazol-5-yl](3,4,5-trimethoxyphenyl)methanone × 2 water × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	STMN4_HUMAN
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain E； PDBConstruct 3–143； UniProt 49–189

Tubulin Tyrosine Ligase

Gallus gallus

UniProt E1BQ43

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 6	Tubulin alpha-1B chain × 2 （Q2XVP4） Tubulin beta-2B chain × 2 （A0A287AGU7） Stathmin-4 × 1 （Q9H169） GUANOSINE-5'-TRIPHOSPHATE × 2 MAGNESIUM ION × 3 CALCIUM ION × 2 GUANOSINE-5'-DIPHOSPHATE × 2 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 2 [2-(4-methyl-1H-indol-3-yl)-1H-imidazol-5-yl](3,4,5-trimethoxyphenyl)methanone × 2 water × 6	Consistent with protein count

Other States of the Same Protein in the Database

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	6o5n
Deposition date deposition_date	2019-03-04
Structure title title	Tubulin-RB3_SLD-TTL in complex with compound 10ab
Keywords keywords	Microtubule Inhibitor, Colchicine, Cancer, CELL CYCLE; CELL CYCLE
Experimental Method method	X-RAY DIFFRACTION

▼

3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

6o5n__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

6o5n__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6o5n__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	55.89 Å
Rg (electron density)	56.85 Å
Total Rg	56.63 Å
Atom count	17435
Residues	2178
Excluded volume	308480 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6o5n__assembly_1__model_1`	hexameric （6）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (11)

Entity 1 Entity 1 polymer

Description description	Tubulin alpha-1B chain
Molecular weight formula_weight	50041.3 kDa
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C
Atom count atom_count	17476

MRECISIHVGQAGVQIGNACWELYCLEHGIQPDGQMPSDKTIGGGDDSFNTFFSETGAGKHVPRAVFVDLEPTVIDEVRTGTYRQLFHPEQLITGKEDAANNYARGHYTIGKEIIDLVLDRIRKLADQCTGLQGFLVFHSFGGGTGSGFTSLLMERLSVDYGKKSKLEFSIYPAPQVSTAVVEPYNSILTTHTTLEHSDCAFMVDNEAIYDICRRNLDIERPTYTNLNRLISQIVSSITASLRFDGALNVDLTEFQTNLVPYPRIHFPLATYAPVISAEKAYHEQLSVAEITNACFEPANQMVKCDPRHGKYMACCLLYRGDVVPKDVNAAIATIKTKRSIQFVDWCPTGFKVGINYQPPTVVPGGDLAKVQRAVCMLSNTTAIAEAWARLDHKFDLMYAKRAFVHWYVGEGMEEGEFSEAREDMAALEKDYEEVGVDSVEGEGEEEGEE

Entity 2 Entity 2 polymer

Description description	Tubulin beta-2B chain
Molecular weight formula_weight	49999.9 kDa
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,D

MREIVHIQAGQCGNQIGAKFWEVISDEHGIDPTGSYHGDSDLQLERINVYYNEATGNKYVPRAILVDLEPGTMDSVRSGPFGQIFRPDNFVFGQSGAGNNWAKGHYTEGAELVDSVLDVVRKESESCDCLQGFQLTHSLGGGTGSGMGTLLISKIREEYPDRIMNTFSVMPSPKVSDTVVEPYNATLSVHQLVENTDETYCIDNEALYDICFRTLKLTTPTYGDLNHLVSATMSGVTTCLRFPGQLNADLRKLAVNMVPFPRLHFFMPGFAPLTSRGSQQYRALTVPELTQQMFDSKNMMAACDPRHGRYLTVAAIFRGRMSMKEVDEQMLNVQNKNSSYFVEWIPNNVKTAVCDIPPRGLKMSATFIGNSTAIQELFKRISEQFTAMFRRKAFLHWYTGEGMDEMEFTEAESNMNDLVSEYQQYQDATADEQGEFEEEEGEDEA

Entity 3 Entity 3 polymer

Description description	Stathmin-4
Molecular weight formula_weight	16844.2 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E

MADMEVIELNKCTSGQSFEVILKPPSFDGVPEFNASLPRRRDPSLEEIQKKLEAAEERRKYQEAELLKHLAEKREHEREVIQKAIEENNNFIKMAKEKLAQKMESNKENREAHLAAMLERLQEKDKHAEEVRKNKELKEEASR

Source Source

Source organism organism	Homo sapiens
Common name common_name	Human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli

Entity 4 Entity 4 polymer

Description description	Tubulin Tyrosine Ligase
Molecular weight formula_weight	44378.5 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	F

MYTFVVRDENSSVYAEVSRLLLATGQWKRLRKDNPRFNLMLGERNRLPFGRLGHEPGLVQLVNYYRGADKLCRKASLVKLIKTSPELSESCTWFPESYVIYPTNLKTPVAPAQNGIRHLINNTRTDEREVFLAAYNRRREGREGNVWIAKSSAGAKGEGILISSEASELLDFIDEQGQVHVIQKYLEKPLLLEPGHRKFDIRSWVLVDHLYNIYLYREGVLRTSSEPYNSANFQDKTCHLTNHCIQKEYSKNYGRYEEGNEMFFEEFNQYLMDALNTTLENSILLQIKHIIRSCLMCIEPAISTKHLHYQSFQLFGFDFMVDEELKVWLIEVNGAPACAQKLYAELCQGIVDVAISSVFPLADTGQKTSQPTSIFIKLHHHHHH

Source Source

Source organism organism	Gallus gallus
Common name common_name	Chicken
NCBI taxonomy ID ncbi_taxonomy_id	9031
Host organism host_organism	Escherichia coli

Entity 5 Entity 5 non-polymer

Description description	GUANOSINE-5'-TRIPHOSPHATE
Molecular weight formula_weight	523.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 6 Entity 6 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 7 Entity 7 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 8 Entity 8 non-polymer

Description description	GUANOSINE-5'-DIPHOSPHATE
Molecular weight formula_weight	443.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 9 Entity 9 non-polymer

Description description	2-(N-MORPHOLINO)-ETHANESULFONIC ACID
Molecular weight formula_weight	195.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 10 Entity 10 non-polymer

Description description	[2-(4-methyl-1H-indol-3-yl)-1H-imidazol-5-yl](3,4,5-trimethoxyphenyl)methanone
Molecular weight formula_weight	391.4 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 11 Entity 11 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	41

▼

6. Fold Classification (SCOP + CATH) 26 domains

SCOP 2.08 (12 domains)

Domain ID domain_id	d6o5na1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.32 — Tubulin nucleotide-binding domain-like
Superfamily Superfamily superfamily	c.32.1 — Tubulin nucleotide-binding domain-like
Family Family family	c.32.1.1 — Tubulin, GTPase domain

Domain ID domain_id	d6o5na2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.79 — Bacillus chorismate mutase-like
Superfamily Superfamily superfamily	d.79.2 — Tubulin C-terminal domain-like
Family Family family	d.79.2.1 — Tubulin, C-terminal domain

Domain ID domain_id	d6o5nb1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.32 — Tubulin nucleotide-binding domain-like
Superfamily Superfamily superfamily	c.32.1 — Tubulin nucleotide-binding domain-like
Family Family family	c.32.1.1 — Tubulin, GTPase domain

Domain ID domain_id	d6o5nb2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.79 — Bacillus chorismate mutase-like
Superfamily Superfamily superfamily	d.79.2 — Tubulin C-terminal domain-like
Family Family family	d.79.2.1 — Tubulin, C-terminal domain

Domain ID domain_id	d6o5nc1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.32 — Tubulin nucleotide-binding domain-like
Superfamily Superfamily superfamily	c.32.1 — Tubulin nucleotide-binding domain-like
Family Family family	c.32.1.1 — Tubulin, GTPase domain

Domain ID domain_id	d6o5nc2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.79 — Bacillus chorismate mutase-like
Superfamily Superfamily superfamily	d.79.2 — Tubulin C-terminal domain-like
Family Family family	d.79.2.1 — Tubulin, C-terminal domain

Domain ID domain_id	d6o5nd1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.32 — Tubulin nucleotide-binding domain-like
Superfamily Superfamily superfamily	c.32.1 — Tubulin nucleotide-binding domain-like
Family Family family	c.32.1.1 — Tubulin, GTPase domain

Domain ID domain_id	d6o5nd2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.79 — Bacillus chorismate mutase-like
Superfamily Superfamily superfamily	d.79.2 — Tubulin C-terminal domain-like
Family Family family	d.79.2.1 — Tubulin, C-terminal domain

Domain ID domain_id	d6o5ne_
Class class	a — All alpha proteins
Fold Fold fold	a.137 — Non-globular all-alpha subunits of globular proteins
Superfamily Superfamily superfamily	a.137.10 — Stathmin
Family Family family	a.137.10.1 — Stathmin

Domain ID domain_id	d6o5nf1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.30 — PreATP-grasp domain
Superfamily Superfamily superfamily	c.30.1 — PreATP-grasp domain
Family Family family	c.30.1.9 — Tubulin tyrosine ligase (TTL) N-terminal domain-like

Domain ID domain_id	d6o5nf2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.142 — ATP-grasp
Superfamily Superfamily superfamily	d.142.1 — Glutathione synthetase ATP-binding domain-like
Family Family family	d.142.1.10 — Tubulin tyrosine ligase (TTL) C-terminal domain-like

Domain ID domain_id	d6o5nf3
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

CATH v4.4 (14 domains)

Domain ID domain_id	6o5nA01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1440 — Tubulin/FtsZ, GTPase domain

Domain ID domain_id	6o5nA02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1330 — 60s Ribosomal Protein L30; Chain: A;
Homologous superfamily homologous superfamily	20 — Tubulin/FtsZ, C-terminal domain

Domain ID domain_id	6o5nA03
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	287 — Helix Hairpins
Homologous superfamily homologous superfamily	600 — Helix hairpin bin

Domain ID domain_id	6o5nB01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1440 — Tubulin/FtsZ, GTPase domain

Domain ID domain_id	6o5nB02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1330 — 60s Ribosomal Protein L30; Chain: A;
Homologous superfamily homologous superfamily	20 — Tubulin/FtsZ, C-terminal domain

Domain ID domain_id	6o5nB03
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	287 — Helix Hairpins
Homologous superfamily homologous superfamily	600 — Helix hairpin bin

Domain ID domain_id	6o5nC01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1440 — Tubulin/FtsZ, GTPase domain

Domain ID domain_id	6o5nC02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1330 — 60s Ribosomal Protein L30; Chain: A;
Homologous superfamily homologous superfamily	20 — Tubulin/FtsZ, C-terminal domain

Domain ID domain_id	6o5nC03
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	287 — Helix Hairpins
Homologous superfamily homologous superfamily	600 — Helix hairpin bin

Domain ID domain_id	6o5nD01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1440 — Tubulin/FtsZ, GTPase domain

Domain ID domain_id	6o5nD02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1330 — 60s Ribosomal Protein L30; Chain: A;
Homologous superfamily homologous superfamily	20 — Tubulin/FtsZ, C-terminal domain

Domain ID domain_id	6o5nD03
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	287 — Helix Hairpins
Homologous superfamily homologous superfamily	600 — Helix hairpin bin

Domain ID domain_id	6o5nE01
Class class	6 — Special
Architecture architecture	10 — Helix non-globular
Topology topology	280 — Methane Monooxygenase Hydroxylase; Chain G, domain 1
Homologous superfamily homologous superfamily	30 —

Domain ID domain_id	6o5nF01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	11480 —

▶

Unit-cell length a length_a	105.301 Å
Unit-cell length b length_b	157.764 Å
Unit-cell length c length_c	182.084 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	3.003 Å
Low-resolution limit resolution_low	41.784 Å
R factor r_factor	0.2046
R_work r_work	0.2024
R_free r_free	0.2452

Tubulin-RB3_SLD-TTL in complex with compound 10ab

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

Tubulin alpha-1B chain

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Tubulin beta-2B chain

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Stathmin-4

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Tubulin Tyrosine Ligase

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

6o5n__assembly_1__model_1

6o5n__assembly_1__model_1 | I(q)

6o5n__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (11)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 polymer

Polymer Polymer

Source Source

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 non-polymer

Entity 9 Entity 9 non-polymer

Entity 10 Entity 10 non-polymer

Entity 11 Entity 11 water

6. Fold Classification (SCOP + CATH) 26 domains

SCOP 2.08 (12 domains)

CATH v4.4 (14 domains)

7. Citations (1)