8yer

Tubulin-RB3_SLD-TTL in complex with compound 4

Method: X-RAY DIFFRACTION

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

Detyrosinated tubulin alpha-1B chain

Sus scrofa

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 chain × 2 （A0A8D0VN39） Stathmin-4 × 1 （P63043） Tubulin--tyrosine ligase × 1 （A0A8C9FGJ1） GUANOSINE-5'-TRIPHOSPHATE × 2 CALCIUM ION × 2 MAGNESIUM ION × 3 6-fluoranyl-4-(6-methoxy-3,4-dihydro-2~{H}-quinolin-1-yl)-~{N}-methyl-quinazolin-2-amine × 2 GUANOSINE-5'-DIPHOSPHATE × 2 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 2 PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER × 1	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 1–440； UniProt 1–440 Author chain C； PDBConstruct 1–440； UniProt 1–440

Tubulin beta chain

Sus scrofa

UniProt A0A8D0VN39

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 6	Detyrosinated tubulin alpha-1B chain × 2 （Q2XVP4） Stathmin-4 × 1 （P63043） Tubulin--tyrosine ligase × 1 （A0A8C9FGJ1） GUANOSINE-5'-TRIPHOSPHATE × 2 CALCIUM ION × 2 MAGNESIUM ION × 3 6-fluoranyl-4-(6-methoxy-3,4-dihydro-2~{H}-quinolin-1-yl)-~{N}-methyl-quinazolin-2-amine × 2 GUANOSINE-5'-DIPHOSPHATE × 2 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 2 PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A0A8D0VN39_PIG
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–431； UniProt 1–431 Author chain D； PDBConstruct 1–431； UniProt 1–431

Stathmin-4

Rattus norvegicus

UniProt P63043

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 6	Detyrosinated tubulin alpha-1B chain × 2 （Q2XVP4） Tubulin beta chain × 2 （A0A8D0VN39） Tubulin--tyrosine ligase × 1 （A0A8C9FGJ1） GUANOSINE-5'-TRIPHOSPHATE × 2 CALCIUM ION × 2 MAGNESIUM ION × 3 6-fluoranyl-4-(6-methoxy-3,4-dihydro-2~{H}-quinolin-1-yl)-~{N}-methyl-quinazolin-2-amine × 2 GUANOSINE-5'-DIPHOSPHATE × 2 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 2 PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER × 1	Consistent with protein count

Other States of the Same Protein in the Database

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

Tubulin--tyrosine ligase

Gallus gallus

UniProt A0A8C9FGJ1

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 6	Detyrosinated tubulin alpha-1B chain × 2 （Q2XVP4） Tubulin beta chain × 2 （A0A8D0VN39） Stathmin-4 × 1 （P63043） GUANOSINE-5'-TRIPHOSPHATE × 2 CALCIUM ION × 2 MAGNESIUM ION × 3 6-fluoranyl-4-(6-methoxy-3,4-dihydro-2~{H}-quinolin-1-yl)-~{N}-methyl-quinazolin-2-amine × 2 GUANOSINE-5'-DIPHOSPHATE × 2 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 2 PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A0A8C9FGJ1_PAVCR
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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	8yer
Deposition date deposition_date	2024-02-23
Last revision last_revision	2025-02-26
Structure title title	Tubulin-RB3_SLD-TTL in complex with compound 4
Keywords keywords	Inhibitor, complex, tubulin, STRUCTURAL PROTEIN; STRUCTURAL PROTEIN
Experimental Method method	X-RAY DIFFRACTION

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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.

8yer__assembly_1__model_1

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

Download this curve (.dat)

8yer__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

8yer__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	55.85 Å
Rg (electron density)	56.75 Å
Total Rg	56.54 Å
Atom count	17484
Residues	2178
Excluded volume	307930 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`8yer__assembly_1__model_1`	hexameric （6）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (11)

Entity 1 Entity 1 polymer

Description description	Detyrosinated tubulin alpha-1B chain
Molecular weight formula_weight	48966.3 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C
Atom count atom_count	17484

MRECISIHVGQAGVQIGNACWELYCLEHGIQPDGQMPSDKTIGGGDDSFNTFFSETGAGKHVPRAVFVDLEPTVIDEVRTGTYRQLFHPEQLITGKEDAANNYARGHYTIGKEIIDLVLDRIRKLADQCTGLQGFLVFHSFGGGTGSGFTSLLMERLSVDYGKKSKLEFSIYPAPQVSTAVVEPYNSILTTHTTLEHSDCAFMVDNEAIYDICRRNLDIERPTYTNLNRLISQIVSSITASLRFDGALNVDLTEFQTNLVPYPRIHFPLATYAPVISAEKAYHEQLSVAEITNACFEPANQMVKCDPRHGKYMACCLLYRGDVVPKDVNAAIATIKTKRSIQFVDWCPTGFKVGINYQPPTVVPGGDLAKVQRAVCMLSNTTAIAEAWARLDHKFDLMYAKRAFVHWYVGEGMEEGEFSEAREDMAALEKDYEEVGVDSV

Source Source

Source organism organism	Sus scrofa
Common name common_name	pig
NCBI taxonomy ID ncbi_taxonomy_id	9823
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Tubulin beta chain
Molecular weight formula_weight	48391.4 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

MREIVHIQAGQCGNQIGAKFWEVISDEHGIDPTGSYHGDSDLQLERINVYYNEATGNKYVPRAILVDLEPGTMDSVRSGPFGQIFRPDNFVFGQSGAGNNWAKGHYTEGAELVDSVLDVVRKESESCDCLQGFQLTHSLGGGTGSGMGTLLISKIREEYPDRIMNTFSVMPSPKVSDTVVEPYNATLSVHQLVENTDETYCIDNEALYDICFRTLKLTTPTYGDLNHLVSATMSGVTTCLRFPGQLNADLRKLAVNMVPFPRLHFFMPGFAPLTSRGSQQYRALTVPELTQQMFDSKNMMAACDPRHGRYLTVAAIFRGRMSMKEVDEQMLNVQNKNSSYFVEWIPNNVKTAVCDIPPRGLKMSATFIGNSTAIQELFKRISEQFTAMFRRKAFLHWYTGEGMDEMEFTEAESNMNDLVSEYQQYQDATAD

Source Source

Source organism organism	Sus scrofa
Common name common_name	pig
NCBI taxonomy ID ncbi_taxonomy_id	9823
Host organism host_organism	Escherichia coli

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	Rattus norvegicus
Common name common_name	Norway rat
NCBI taxonomy ID ncbi_taxonomy_id	10116
Host organism host_organism	Escherichia coli

Entity 4 Entity 4 polymer

Description description	Tubulin--tyrosine ligase
Molecular weight formula_weight	43825.9 kDa
EC 编号 ec_number	6.3.2.25
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	F

MYTFVVRDENSSVYAEVSRLLLATGQWKRLRKDNPRFNLMLGERNRLPFGRLGHEPGLVQLVNYYRGADKLCRKASLVKLIKTSPELSESCTWFPESYVIYPTNLKTPVAPAQNGIRHLINNTRTDEREVFLAAYNRRREGREGNVWIAKSSAGAKGEGILISSEASELLDFIDEQGQVHVIQKYLEKPLLLEPGHRKFDIRSWVLVDHLYNIYLYREGVLRTSSEPYNSANFQDKTCHLTNHCIQKEYSKNYGRYEEGNEMFFEEFNQYLMDALNTTLENSILLQIKHIIRSCLMCIEPAISTKHLHYQSFQLFGFDFMVDEELKVWLIEVNGAPACAQKLYAELCQGIVDVAISSVFPLADTGQKTSQPTSIFIKLHH

Source Source

Source organism organism	Gallus gallus
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	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 7 Entity 7 non-polymer

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

Entity 8 Entity 8 non-polymer

Description description	6-fluoranyl-4-(6-methoxy-3,4-dihydro-2~{H}-quinolin-1-yl)-~{N}-methyl-quinazolin-2-amine
Molecular weight formula_weight	338.4 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 9 Entity 9 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 10 Entity 10 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 11 Entity 11 non-polymer

Description description	PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER
Molecular weight formula_weight	505.2 kDa
Source method src_method	syn
Copy count entity_count	1

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Unit-cell length a length_a	105.150 Å
Unit-cell length b length_b	157.260 Å
Unit-cell length c length_c	181.640 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	2.710 Å
Low-resolution limit resolution_low	39.700 Å
R factor r_factor	0.2239
R_work r_work	0.2224
R_free r_free	0.2859

Tubulin-RB3_SLD-TTL in complex with compound 4

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

Detyrosinated 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 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

8yer__assembly_1__model_1

8yer__assembly_1__model_1 | I(q)

8yer__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

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

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 non-polymer

7. Citations (1)