4j7b

Crystal structure of polo-like kinase 1

Method: X-RAY DIFFRACTION

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

Polo-like kinase

Danio rerio

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	205 kDa microtubule-associated protein × 1 （P23226） water × 3	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 3	205 kDa microtubule-associated protein × 1 （P23226） water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q6DRK7_DANRE
Isoform	—
PDB entities	1, 2
Chains and sequence ranges	Author chain A； PDBConstruct 3–297； UniProt 18–312 Author chain D； PDBConstruct 3–297； UniProt 18–312 Author chain B； PDBConstruct 2–237； UniProt 360–595 Author chain E； PDBConstruct 2–237； UniProt 360–595

205 kDa microtubule-associated protein

Drosophila melanogaster

UniProt P23226

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	Polo-like kinase × 1 （Q6DRK7） Polo-like kinase × 1 （Q6DRK7） water × 3	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 3	Polo-like kinase × 1 （Q6DRK7） Polo-like kinase × 1 （Q6DRK7） water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	MA205_DROME
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 9–58； UniProt 276–325 Author chain F； PDBConstruct 9–58； UniProt 276–325

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	4j7b
Deposition date deposition_date	2013-02-13
Structure title title	Crystal structure of polo-like kinase 1
Keywords keywords	First complex structure of KD and PBD domain, regulator of mitosis, phosphorylated target protein, 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.

4j7b__assembly_2__model_1

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

Download this curve (.dat)

4j7b__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4j7b__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	26.67 Å
Rg (electron density)	25.66 Å
Total Rg	26.53 Å
Atom count	4394
Residues	543
Excluded volume	78663 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4j7b__assembly_1__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`4j7b__assembly_2__model_1`	trimeric （3）	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	Polo-like kinase
Molecular weight formula_weight	34106.9 kDa
EC 编号 ec_number	2.7.11.21
Mutation mutation	D162N, E192F
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,D
Atom count atom_count	9170

MGPKSAPLKEIPDVLVDPRTMKRYMRGRFLGKGGFAKCYEITDMDTKEVFAGKVVPKSMLLKPHQKEKMSTEIAIHKSLDNPHVVGFHGFFEDDDFVYVVLEICRRRSLLELHKRRKAVTEPEARYFMRQTIQGVQYLHNNRVIHRNLKLGNLFLNDDMDVKIGDFGLATKIEFDGFRKKTLCGTPNYIAPEVLCKKGHSFEVDIWSLGCILYTLLVGKPPFETSCLKETYIRIKKNEYSVPRHINPVASALIRRMLHADPTLRPSVAELLTDEFFTSGYAPMRLPTSCLTVPPRFS

Source Source

Source organism organism	Danio rerio
Common name common_name	leopard danio,zebra danio,zebra fish
NCBI taxonomy ID ncbi_taxonomy_id	7955
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Polo-like kinase
Molecular weight formula_weight	27206.2 kDa
EC 编号 ec_number	2.7.11.21
Mutation mutation	D384G
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

MQPDTHLTDMLQQLAVVNAAKPSDRGFIRQEEAEDPACIPVFWISKWVDYSDKYGLGYQLSDNSVGVLFNDSTRLIMCADGDSLQYIDRNSLESYLSVRSYPSALSKKITLLKYFRNYMSEHLLKAGANITPREGDELTRLPYLRHWFRTKSAIVLHLSNGTVQINFFQDHTKLILCPLMGAVTYINEKREFYTYKMTLIEEFGCCKELASRLRYARNMVEKLMACKSSTTAATSAR

Source Source

Source organism organism	Danio rerio
Common name common_name	leopard danio,zebra danio,zebra fish
NCBI taxonomy ID ncbi_taxonomy_id	7955
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 polymer

Description description	205 kDa microtubule-associated protein
Molecular weight formula_weight	6686.3 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

MGHHHHHHLDDLVAESPRKEFARINMDGIAVPDEREFDIEADMRPHELEQESDTFGAG

Source Source

Source organism organism	Drosophila melanogaster
Common name common_name	Fruit fly
NCBI taxonomy ID ncbi_taxonomy_id	7227
Host organism host_organism	Escherichia coli

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	360

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6. Fold Classification (SCOP + CATH) 14 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d4j7ba_
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.144.1.0 — automated matches

Domain ID domain_id	d4j7bb1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.223 — Polo-box domain
Superfamily Superfamily superfamily	d.223.1 — Polo-box domain
Family Family family	d.223.1.2 — Polo-box duplicated region

Domain ID domain_id	d4j7bb2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.223 — Polo-box domain
Superfamily Superfamily superfamily	d.223.1 — Polo-box domain
Family Family family	d.223.1.2 — Polo-box duplicated region

Domain ID domain_id	d4j7bd_
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.144.1.0 — automated matches

Domain ID domain_id	d4j7be1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.223 — Polo-box domain
Superfamily Superfamily superfamily	d.223.1 — Polo-box domain
Family Family family	d.223.1.2 — Polo-box duplicated region

Domain ID domain_id	d4j7be2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.223 — Polo-box domain
Superfamily Superfamily superfamily	d.223.1 — Polo-box domain
Family Family family	d.223.1.2 — Polo-box duplicated region

CATH v4.4 (8 domains)

Domain ID domain_id	4j7bA01
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	4j7bA02
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	4j7bB01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1120 — Arylsulfatase, C-terminal domain
Homologous superfamily homologous superfamily	30 — POLO box domain

Domain ID domain_id	4j7bB02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1120 — Arylsulfatase, C-terminal domain
Homologous superfamily homologous superfamily	30 — POLO box domain

Domain ID domain_id	4j7bD01
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	4j7bD02
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	4j7bE01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1120 — Arylsulfatase, C-terminal domain
Homologous superfamily homologous superfamily	30 — POLO box domain

Domain ID domain_id	4j7bE02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1120 — Arylsulfatase, C-terminal domain
Homologous superfamily homologous superfamily	30 — POLO box domain

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Unit-cell length a length_a	47.681 Å
Unit-cell length b length_b	57.453 Å
Unit-cell length c length_c	125.736 Å
Unit-cell angle α angle_alpha	89.15 °
Unit-cell angle β angle_beta	89.84 °
Unit-cell angle γ angle_gamma	72.38 °
Molecules per unit cell Z z_pdb	2

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

Resolution resolution	2.300 Å
Low-resolution limit resolution_low	25.000 Å
R factor r_factor	0.2077
R_work r_work	0.2048
R_free r_free	0.2635

Crystal structure of polo-like kinase 1

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

Polo-like kinase

State in the Current Structure

Other States of the Same Protein in the Database

205 kDa microtubule-associated protein

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

4j7b__assembly_2__model_1

4j7b__assembly_2__model_1 | I(q)

4j7b__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 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 14 domains

SCOP 2.08 (6 domains)

CATH v4.4 (8 domains)

7. Citations (1)

Crystal structure of polo-like kinase 1

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

Polo-like kinase

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

205 kDa microtubule-associated protein

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

4j7b__assembly_2__model_1

4j7b__assembly_2__model_1 | I(q)

4j7b__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 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 14 domains

SCOP 2.08 (6 domains)

CATH v4.4 (8 domains)

7. Citations (1)