SAXSdb — 5k3y

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

Aurora kinase B-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） ;N-methyl-N-(1-methylpiperidin-4-yl)-4-{[4-({(1R,2S)-2-[(propan-2-yl)carbamoyl]cyclopentyl}amino)-5-(trifluoromethyl)pyrimidin-2-yl]amino}benzamide ; × 1 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	Inner centromere protein A × 1 （O13024） ;N-methyl-N-(1-methylpiperidin-4-yl)-4-{[4-({(1R,2S)-2-[(propan-2-yl)carbamoyl]cyclopentyl}amino)-5-(trifluoromethyl)pyrimidin-2-yl]amino}benzamide ; × 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 2–280； UniProt 78–356 Author chain B； PDBConstruct 2–280； UniProt 78–356

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	Aurora kinase B-A × 1 （Q6DE08） ;N-methyl-N-(1-methylpiperidin-4-yl)-4-{[4-({(1R,2S)-2-[(propan-2-yl)carbamoyl]cyclopentyl}amino)-5-(trifluoromethyl)pyrimidin-2-yl]amino}benzamide ; × 1 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	Aurora kinase B-A × 1 （Q6DE08） ;N-methyl-N-(1-methylpiperidin-4-yl)-4-{[4-({(1R,2S)-2-[(propan-2-yl)carbamoyl]cyclopentyl}amino)-5-(trifluoromethyl)pyrimidin-2-yl]amino}benzamide ; × 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 2–59； UniProt 790–847 Author chain D； PDBConstruct 2–59； UniProt 790–847

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	5k3y
Deposition date deposition_date	2016-05-20
Structure title title	Crystal structure of AuroraB/INCENP in complex with BI 811283
Keywords keywords	Kinase, Inhibitor, transferase; 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.

5k3y__assembly_2__model_1

Assembly 2 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

5k3y__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5k3y__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	21.64 Å
Rg (electron density)	20.61 Å
Total Rg	21.60 Å
Atom count	2643
Residues	312
Excluded volume	47296 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5k3y__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`5k3y__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	Aurora kinase B-A
Molecular weight formula_weight	33104.4 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	5878

GTALAEMPKRKFTIDDFDIVRPLGKGKFGNVYLAREKQNKFIMALKVLFKSQLEKEGVEHQLRREIEIQSHLRHPNILRMYNYFHDRKRIYLMLEFAPRGELYKELQKHGRFDEQRSATFMEELADALHYCHERKVIHRDIKPENLLMGYKGELKIADFGWSVHAPSLRRRTMCGTLDYLPPEMIEGKTHDEKVDLWCAGVLCYEFLVGMPPFDSPSHTETHRRIVNVDLKFPPFLSDGSKDLISKLLRYHPPQRLPLKGVMEHPWVKANSRRVLPPVYQ

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	Enterobacteria phage L1

Entity 2 Entity 2 polymer

Description description	Inner centromere protein A
Molecular weight formula_weight	7028.1 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

MDESQPRKPIPAWASGNLLTQAIRQQYYKPIDVDRMYGTIDSPKLEELFNKSKPRYFKR

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	Enterobacteria phage L1

Entity 3 Entity 3 non-polymer

Description description	;N-methyl-N-(1-methylpiperidin-4-yl)-4-{[4-({(1R,2S)-2-[(propan-2-yl)carbamoyl]cyclopentyl}amino)-5-(trifluoromethyl)pyrimidin-2-yl]amino}benzamide ;
Molecular weight formula_weight	561.6 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	612

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6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d5k3ya_
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	d5k3yb_
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 (4 domains)

Domain ID domain_id	5k3yA01
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	5k3yA02
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	5k3yB01
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	5k3yB02
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

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Unit-cell length a length_a	45.907 Å
Unit-cell length b length_b	67.295 Å
Unit-cell length c length_c	116.618 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	96.19 °
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	1.600 Å
Low-resolution limit resolution_low	32.000 Å
R factor r_factor	0.1810
R_work r_work	0.1800
R_free r_free	0.2010

Crystal structure of AuroraB/INCENP in complex with BI 811283

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

Aurora kinase B-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

5k3y__assembly_2__model_1

5k3y__assembly_2__model_1 | I(q)

5k3y__assembly_2__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) 6 domains

SCOP 2.08 (2 domains)

CATH v4.4 (4 domains)

7. Citations (1)

Crystal structure of AuroraB/INCENP in complex with BI 811283

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

Aurora kinase B-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

5k3y__assembly_2__model_1

5k3y__assembly_2__model_1 | I(q)

5k3y__assembly_2__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) 6 domains

SCOP 2.08 (2 domains)

CATH v4.4 (4 domains)

7. Citations (1)