SAXSdb — 5dmv

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

Serine/threonine-protein kinase PLK1

Mus musculus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	F-box only protein 43 × 1 （Q8CDI2） NICKEL (II) ION × 3 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PLK1_MOUSE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain C； PDBConstruct 1–237； UniProt 367–603

F-box only protein 43

OrganismNot specified

UniProt Q8CDI2

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 PLK1 × 1 （Q07832） NICKEL (II) ION × 3 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	FBX43_MOUSE
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain D； PDBConstruct 1–32； UniProt 146–177

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	5dmv
Deposition date deposition_date	2015-09-09
Structure title title	Polo-box domain of Mouse Polo-like kinase 1 complexed with Emi2 (146-177)
Keywords keywords	Polo-box, PLK1, Emi2, meiosis, TRANSFERASE-METAL BINDING PROTEIN complex; TRANSFERASE/METAL BINDING PROTEIN
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.

5dmv__assembly_1__model_1

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

Download this curve (.dat)

5dmv__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5dmv__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	19.60 Å
Rg (electron density)	18.38 Å
Total Rg	19.46 Å
Atom count	1937
Residues	240
Excluded volume	34593 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5dmv__assembly_1__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 PLK1
Molecular weight formula_weight	27243.0 kDa
EC 编号 ec_number	2.7.11.21
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C
Atom count atom_count	1978

NEAIECHLSDLLQQLTSVNASKPSERGLVRQEEAEDPACIPIFWVSKWVDYSDKYGLGYQLCDNSVGVLFNDSTRLILYNDGDSLQYIERDGTESYLTVSSHPNSLMKKITLLNYFRNYMSEHLLKAGANITPREGDELARLPYLRTWFRTRSAIILHLSNGTVQINFFQDHTKLILCPLMAAVTYINEKRDFQTYRLSLLEEYGCCKELASRLRYARTMVDKLLSSRSASNRLKAS

Source Source

Source organism organism	Mus musculus
Common name common_name	Mouse
NCBI taxonomy ID ncbi_taxonomy_id	10090
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	F-box only protein 43
Molecular weight formula_weight	3707.9 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D

SPLVTSTIKTEDVVSNSQNSRLHFSQHKTSTI

Entity 3 Entity 3 non-polymer

Description description	NICKEL (II) ION
Molecular weight formula_weight	58.7 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	38

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6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	5dmvC01
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	5dmvC02
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	35.627 Å
Unit-cell length b length_b	63.329 Å
Unit-cell length c length_c	56.831 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	97.20 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	2

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

Resolution resolution	2.499 Å
Low-resolution limit resolution_low	28.414 Å
R factor r_factor	0.2156
R_work r_work	0.2117
R_free r_free	0.2909

Polo-box domain of Mouse Polo-like kinase 1 complexed with Emi2 (146-177)

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

Serine/threonine-protein kinase PLK1

State in the Current Structure

Other States of the Same Protein in the Database

F-box only protein 43

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

5dmv__assembly_1__model_1

5dmv__assembly_1__model_1 | I(q)

5dmv__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

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)

Polo-box domain of Mouse Polo-like kinase 1 complexed with Emi2 (146-177)

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

Serine/threonine-protein kinase PLK1

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

F-box only protein 43

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

5dmv__assembly_1__model_1

5dmv__assembly_1__model_1 | I(q)

5dmv__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

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)