7e4r

Crystal structure of tubulin in complex with D-DM1-SMe

Method: X-RAY DIFFRACTION

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

Tubulin alpha-1B chain

Bos taurus

UniProt P81947

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 （Q6B856） Stathmin-4 × 1 （P63043） Tubulin tyrosine ligase × 1 （E1BQ43） GUANOSINE-5'-TRIPHOSPHATE × 3 MAGNESIUM ION × 4 CALCIUM ION × 2 GUANOSINE-5'-DIPHOSPHATE × 1 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 ;(10E,12E)-86-chloro-14-hydroxy-85,14-dimethoxy-33,2,7,10-tetramethyl-12,6-dioxo-7-aza-1(6,4)-oxazinana-3(2,3)-oxirana-8(1,3)-benzenacyclotetradecaphane-10,12-dien-4-yl N-methyl-N-(3-(methylsulfinothioyl)propanoyl)-D-alaninate ; × 1 PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER × 1 water × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	TBA1B_BOVIN
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-2B chain

Bos taurus

UniProt Q6B856

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 （P81947） Stathmin-4 × 1 （P63043） Tubulin tyrosine ligase × 1 （E1BQ43） GUANOSINE-5'-TRIPHOSPHATE × 3 MAGNESIUM ION × 4 CALCIUM ION × 2 GUANOSINE-5'-DIPHOSPHATE × 1 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 ;(10E,12E)-86-chloro-14-hydroxy-85,14-dimethoxy-33,2,7,10-tetramethyl-12,6-dioxo-7-aza-1(6,4)-oxazinana-3(2,3)-oxirana-8(1,3)-benzenacyclotetradecaphane-10,12-dien-4-yl N-methyl-N-(3-(methylsulfinothioyl)propanoyl)-D-alaninate ; × 1 PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER × 1 water × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	TBB2B_BOVIN
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	Tubulin alpha-1B chain × 2 （P81947） Tubulin beta-2B chain × 2 （Q6B856） Tubulin tyrosine ligase × 1 （E1BQ43） GUANOSINE-5'-TRIPHOSPHATE × 3 MAGNESIUM ION × 4 CALCIUM ION × 2 GUANOSINE-5'-DIPHOSPHATE × 1 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 ;(10E,12E)-86-chloro-14-hydroxy-85,14-dimethoxy-33,2,7,10-tetramethyl-12,6-dioxo-7-aza-1(6,4)-oxazinana-3(2,3)-oxirana-8(1,3)-benzenacyclotetradecaphane-10,12-dien-4-yl N-methyl-N-(3-(methylsulfinothioyl)propanoyl)-D-alaninate ; × 1 PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER × 1 water × 6	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 1–138； UniProt 50–187

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 （P81947） Tubulin beta-2B chain × 2 （Q6B856） Stathmin-4 × 1 （P63043） GUANOSINE-5'-TRIPHOSPHATE × 3 MAGNESIUM ION × 4 CALCIUM ION × 2 GUANOSINE-5'-DIPHOSPHATE × 1 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 ;(10E,12E)-86-chloro-14-hydroxy-85,14-dimethoxy-33,2,7,10-tetramethyl-12,6-dioxo-7-aza-1(6,4)-oxazinana-3(2,3)-oxirana-8(1,3)-benzenacyclotetradecaphane-10,12-dien-4-yl N-methyl-N-(3-(methylsulfinothioyl)propanoyl)-D-alaninate ; × 1 PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER × 1 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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	7e4r
Deposition date deposition_date	2021-02-15
Structure title title	Crystal structure of tubulin in complex with D-DM1-SMe
Keywords keywords	microtubule assembly inhibitors, STRUCTURAL PROTEIN-INHIBITOR complex; STRUCTURAL PROTEIN/INHIBITOR
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.

7e4r__assembly_1__model_1

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

Download this curve (.dat)

7e4r__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

7e4r__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	56.17 Å
Rg (electron density)	57.11 Å
Total Rg	56.94 Å
Atom count	34338
Residues	2180
Excluded volume	309380 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`7e4r__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 (12)

Entity 1 Entity 1 polymer

Description description	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	34660

MRECISIHVGQAGVQIGNACWELYCLEHGIQPDGQMPSDKTIGGGDDSFNTFFSETGAGKHVPRAVFVDLEPTVIDEVRTGTYRQLFHPEQLITGKEDAANNYARGHYTIGKEIIDLVLDRIRKLADQCTGLQGFLVFHSFGGGTGSGFTSLLMERLSVDYGKKSKLEFSIYPAPQVSTAVVEPYNSILTTHTTLEHSDCAFMVDNEAIYDICRRNLDIERPTYTNLNRLISQIVSSITASLRFDGALNVDLTEFQTNLVPYPRIHFPLATYAPVISAEKAYHEQLSVAEITNACFEPANQMVKCDPRHGKYMACCLLYRGDVVPKDVNAAIATIKTKRSIQFVDWCPTGFKVGINYQPPTVVPGGDLAKVQRAVCMLSNTTAIAEAWARLDHKFDLMYAKRAFVHWYVGEGMEEGEFSEAREDMAALEKDYEEVGVDSV

Source Source

Source organism organism	Bos taurus
Common name common_name	Bovine
NCBI taxonomy ID ncbi_taxonomy_id	9913
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Tubulin beta-2B 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	Bos taurus
Common name common_name	Bovine
NCBI taxonomy ID ncbi_taxonomy_id	9913
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 polymer

Description description	Stathmin-4
Molecular weight formula_weight	16282.5 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E

MEVIELNKCTSGQSFEVILKPPSFDGVPEFNASLPRRRDPSLEEIQKKLEAAEERRKYQEAELLKHLAEKREHEREVIQKAIEENNNFIKMAKEKLAQKMESNKENREAHLAAMLERLQEKDKHAEEVRKNKELKEEA

Source Source

Source organism organism	Rattus norvegicus
Common name common_name	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
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
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	3

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	4

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	1

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	1

Entity 10 Entity 10 non-polymer

Description description	;(10E,12E)-86-chloro-14-hydroxy-85,14-dimethoxy-33,2,7,10-tetramethyl-12,6-dioxo-7-aza-1(6,4)-oxazinana-3(2,3)-oxirana-8(1,3)-benzenacyclotetradecaphane-10,12-dien-4-yl N-methyl-N-(3-(methylsulfinothioyl)propanoyl)-D-alaninate ;
Molecular weight formula_weight	784.4 kDa
Source method src_method	syn
Copy count entity_count	1

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

Entity 12 Entity 12 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	322

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6. Fold Classification (SCOP + CATH) 13 domains

SCOP 2.08 (12 domains)

Domain ID domain_id	d7e4ra1
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	d7e4ra2
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	d7e4rb1
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	d7e4rb2
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	d7e4rc1
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	d7e4rc2
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	d7e4rd1
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	d7e4rd2
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	d7e4re_
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	d7e4rf1
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	d7e4rf2
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	d7e4rf3
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 (1 domains)

Domain ID domain_id	7e4rF01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	11480 —

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Unit-cell length a length_a	104.982 Å
Unit-cell length b length_b	157.229 Å
Unit-cell length c length_c	182.574 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	2.597 Å
Low-resolution limit resolution_low	45.452 Å
R factor r_factor	0.2246
R_work r_work	0.2240
R_free r_free	0.2652

Crystal structure of tubulin in complex with D-DM1-SMe

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

7e4r__assembly_1__model_1

7e4r__assembly_1__model_1 | I(q)

7e4r__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 (12)

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

Entity 12 Entity 12 water

6. Fold Classification (SCOP + CATH) 13 domains

SCOP 2.08 (12 domains)

CATH v4.4 (1 domains)

7. Citations (1)