7e4p

Crystal structure of tubulin in complex with Ansamitocin P3

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 × 5 CALCIUM ION × 2 GLYCEROL × 1 GUANOSINE-5'-DIPHOSPHATE × 1 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 ;(1S,2S,3S,5S,6S,16Z,18Z,20R,21S)-11-chloro-21-hydroxy-12,20-dimethoxy-2,5,9,16-tetramethyl-8,23-dioxo-4,24-dioxa-9,22-diazatetracyclo[19.3.1.1~10,14~.0~3,5~]hexacosa-10(26),11,13,16,18-pentaen-6-yl 2-methylpropanoate ; × 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 × 5 CALCIUM ION × 2 GLYCEROL × 1 GUANOSINE-5'-DIPHOSPHATE × 1 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 ;(1S,2S,3S,5S,6S,16Z,18Z,20R,21S)-11-chloro-21-hydroxy-12,20-dimethoxy-2,5,9,16-tetramethyl-8,23-dioxo-4,24-dioxa-9,22-diazatetracyclo[19.3.1.1~10,14~.0~3,5~]hexacosa-10(26),11,13,16,18-pentaen-6-yl 2-methylpropanoate ; × 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 × 5 CALCIUM ION × 2 GLYCEROL × 1 GUANOSINE-5'-DIPHOSPHATE × 1 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 ;(1S,2S,3S,5S,6S,16Z,18Z,20R,21S)-11-chloro-21-hydroxy-12,20-dimethoxy-2,5,9,16-tetramethyl-8,23-dioxo-4,24-dioxa-9,22-diazatetracyclo[19.3.1.1~10,14~.0~3,5~]hexacosa-10(26),11,13,16,18-pentaen-6-yl 2-methylpropanoate ; × 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 × 5 CALCIUM ION × 2 GLYCEROL × 1 GUANOSINE-5'-DIPHOSPHATE × 1 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 ;(1S,2S,3S,5S,6S,16Z,18Z,20R,21S)-11-chloro-21-hydroxy-12,20-dimethoxy-2,5,9,16-tetramethyl-8,23-dioxo-4,24-dioxa-9,22-diazatetracyclo[19.3.1.1~10,14~.0~3,5~]hexacosa-10(26),11,13,16,18-pentaen-6-yl 2-methylpropanoate ; × 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	7e4p
Deposition date deposition_date	2021-02-14
Structure title title	Crystal structure of tubulin in complex with Ansamitocin P3
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.

7e4p__assembly_1__model_1

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

Download this curve (.dat)

7e4p__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

7e4p__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	56.14 Å
Rg (electron density)	57.11 Å
Total Rg	56.92 Å
Atom count	34381
Residues	2182
Excluded volume	309710 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`7e4p__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 (13)

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	35098

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	5

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	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	1

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	1

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	1

Entity 11 Entity 11 non-polymer

Description description	;(1S,2S,3S,5S,6S,16Z,18Z,20R,21S)-11-chloro-21-hydroxy-12,20-dimethoxy-2,5,9,16-tetramethyl-8,23-dioxo-4,24-dioxa-9,22-diazatetracyclo[19.3.1.1~10,14~.0~3,5~]hexacosa-10(26),11,13,16,18-pentaen-6-yl 2-methylpropanoate ;
Molecular weight formula_weight	635.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 12 Entity 12 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 13 Entity 13 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	717

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6. Fold Classification (SCOP + CATH) 14 domains

CATH v4.4 (14 domains)

Domain ID domain_id	7e4pA01
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	7e4pA02
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	7e4pA03
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	7e4pB01
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	7e4pB02
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	7e4pB03
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	7e4pC01
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	7e4pC02
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	7e4pC03
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	7e4pD01
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	7e4pD02
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	7e4pD03
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	7e4pF01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	11480 —

Domain ID domain_id	7e4pF02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	470 — D-amino Acid Aminotransferase; Chain A, domain 1
Homologous superfamily homologous superfamily	20 — ATP-grasp fold, B domain

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Unit-cell length a length_a	105.399 Å
Unit-cell length b length_b	158.569 Å
Unit-cell length c length_c	181.760 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	2.400 Å
Low-resolution limit resolution_low	47.248 Å
R factor r_factor	0.2131
R_work r_work	0.2130
R_free r_free	0.2294

Crystal structure of tubulin in complex with Ansamitocin P3

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

7e4p__assembly_1__model_1

7e4p__assembly_1__model_1 | I(q)

7e4p__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 (13)

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 non-polymer

Entity 13 Entity 13 water

6. Fold Classification (SCOP + CATH) 14 domains

CATH v4.4 (14 domains)

7. Citations (1)