SAXSdb — 2vgp

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

SERINE/THREONINE-PROTEIN KINASE 12-A

XENOPUS LAEVIS

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	INNER CENTROMERE PROTEIN A × 1 （O13024） 4-[(5-bromo-1,3-thiazol-2-yl)amino]-N-methylbenzamide × 1 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	INNER CENTROMERE PROTEIN A × 1 （O13024） 4-[(5-bromo-1,3-thiazol-2-yl)amino]-N-methylbenzamide × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	AUKBA_XENLA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–284； UniProt 78–361 Author chain B； PDBConstruct 1–284； UniProt 78–361

INNER CENTROMERE PROTEIN A

XENOPUS LAEVIS

UniProt O13024

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	SERINE/THREONINE-PROTEIN KINASE 12-A × 1 （Q6DE08） 4-[(5-bromo-1,3-thiazol-2-yl)amino]-N-methylbenzamide × 1 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	SERINE/THREONINE-PROTEIN KINASE 12-A × 1 （Q6DE08） 4-[(5-bromo-1,3-thiazol-2-yl)amino]-N-methylbenzamide × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	INCEA_XENLA
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 1–43； UniProt 798–840 Author chain D； PDBConstruct 1–43； UniProt 798–840

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	2vgp
Deposition date deposition_date	2007-11-15
Structure title title	Crystal structure of Aurora B kinase in complex with a aminothiazole inhibitor
Keywords keywords	;NUCLEOTIDE-BINDING, SERINE/THREONINE-PROTEIN KINASE, ATP-BINDING, TRANSFERASE, COILED COIL, CELL DIVISION, KINASE, CANCER, INCENP, NUCLEUS, MITOSIS, AURORA B, METAL-BINDING, AMINOTHIAZOLE, PHOSPHORYLATION, MAGNESIUM, CELL CYCLE, CENTROMERE, MICROTUBULE ;; TRANSFERASE
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.

2vgp__assembly_1__model_1

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

Download this curve (.dat)

2vgp__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2vgp__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	21.53 Å
Rg (electron density)	20.47 Å
Total Rg	21.37 Å
Atom count	2585
Residues	308
Excluded volume	46145 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2vgp__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2vgp__assembly_2__model_1`	dimeric （2）	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 (4)

Entity 1 Entity 1 polymer

Description description	SERINE/THREONINE-PROTEIN KINASE 12-A
Molecular weight formula_weight	33537.9 kDa
EC 编号 ec_number	2.7.11.1
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	6015

TALAEMPKRKFTIDDFDIGRPLGKGKFGNVYLAREKQNKFIMALKVLFKSQLEKEGVEHQLRREIEIQSHLRHPNILRMYNYFHDRKRIYLMLEFAPRGELYKELQKHGRFDEQRSATFMEELADALHYCHERKVIHRDIKPENLLMGYKGELKIADFGWSVHAPSLRRRTMCGTLDYLPPEMIEGKTHDEKVDLWCAGVLCYEFLVGMPPFDSPSHTETHRRIVNVDLKFPPFLSDGSKDLISKLLRYHPPQRLPLKGVMEHPWVKANSRRVLPPVYQSTQSK

Source Source

Source organism organism	XENOPUS LAEVIS
Common name common_name	AFRICAN CLAWED FROG
NCBI taxonomy ID ncbi_taxonomy_id	8355
Host organism host_organism	ESCHERICHIA COLI

Entity 2 Entity 2 polymer

Description description	INNER CENTROMERE PROTEIN A
Molecular weight formula_weight	4976.6 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

IPAWASGNLLTQAIRQQYYKPIDVDRMYGTIDSPKLEELFNKS

Source Source

Source organism organism	XENOPUS LAEVIS
Common name common_name	AFRICAN CLAWED FROG
NCBI taxonomy ID ncbi_taxonomy_id	8355
Host organism host_organism	ESCHERICHIA COLI

Entity 3 Entity 3 non-polymer

Description description	4-[(5-bromo-1,3-thiazol-2-yl)amino]-N-methylbenzamide
Molecular weight formula_weight	312.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	729

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6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d2vgpa_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.144 — Protein kinase-like (PK-like)
Superfamily Superfamily superfamily	d.144.1 — Protein kinase-like (PK-like)
Family Family family	d.144.1.7 — Protein kinases, catalytic subunit

Domain ID domain_id	d2vgpb_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.144 — Protein kinase-like (PK-like)
Superfamily Superfamily superfamily	d.144.1 — Protein kinase-like (PK-like)
Family Family family	d.144.1.7 — Protein kinases, catalytic subunit

CATH v4.4 (6 domains)

Domain ID domain_id	2vgpA01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	200 — Phosphorylase Kinase; domain 1
Homologous superfamily homologous superfamily	20 — Phosphorylase Kinase; domain 1

Domain ID domain_id	2vgpA02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	510 — Transferase(Phosphotransferase); domain 1
Homologous superfamily homologous superfamily	10 — Transferase(Phosphotransferase) domain 1

Domain ID domain_id	2vgpB01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	200 — Phosphorylase Kinase; domain 1
Homologous superfamily homologous superfamily	20 — Phosphorylase Kinase; domain 1

Domain ID domain_id	2vgpB02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	510 — Transferase(Phosphotransferase); domain 1
Homologous superfamily homologous superfamily	10 — Transferase(Phosphotransferase) domain 1

Domain ID domain_id	2vgpC01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	2230 —

Domain ID domain_id	2vgpD00
Class class	6 — Special
Architecture architecture	10 — Helix non-globular
Topology topology	250 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	2990 —

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Unit-cell length a length_a	45.958 Å
Unit-cell length b length_b	67.196 Å
Unit-cell length c length_c	117.263 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	96.67 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	1.700 Å
Low-resolution limit resolution_low	25.000 Å
R factor r_factor	0.2080
R_work r_work	0.2060
R_free r_free	0.2430

Crystal structure of Aurora B kinase in complex with a aminothiazole inhibitor

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

SERINE/THREONINE-PROTEIN KINASE 12-A

State in the Current Structure

Other States of the Same Protein in the Database

INNER CENTROMERE PROTEIN A

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

2vgp__assembly_1__model_1

2vgp__assembly_1__model_1 | I(q)

2vgp__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (2 domains)

CATH v4.4 (6 domains)

7. Citations (1)

Crystal structure of Aurora B kinase in complex with a aminothiazole inhibitor

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

SERINE/THREONINE-PROTEIN KINASE 12-A

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

INNER CENTROMERE PROTEIN A

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

2vgp__assembly_1__model_1

2vgp__assembly_1__model_1 | I(q)

2vgp__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (2 domains)

CATH v4.4 (6 domains)

7. Citations (1)