7v3x

Crystal Structure of Cyanobacterial Circadian Clock Protein KaiC

Method: X-RAY DIFFRACTION

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

Circadian clock protein kinase KaiC

Synechococcus elongatus (strain PCC 7942 / FACHB-805)

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 6	ADENOSINE-5'-TRIPHOSPHATE × 12 MAGNESIUM ION × 12 water × 6	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 6	ADENOSINE-5'-TRIPHOSPHATE × 12 MAGNESIUM ION × 12 water × 6	Consistent with protein count
3	Protein homooligomer	Homooligomer	Protein 6	ADENOSINE-5'-TRIPHOSPHATE × 11 MAGNESIUM ION × 9 ADENOSINE-5'-DIPHOSPHATE × 1 water × 6	Consistent with protein count
4	Protein homooligomer	Homooligomer	Protein 6	ADENOSINE-5'-TRIPHOSPHATE × 10 MAGNESIUM ION × 3 ADENOSINE-5'-DIPHOSPHATE × 2 water × 5	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	KAIC_SYNE7
Isoform	—
PDB entities	1, 2
Chains and sequence ranges	Author chain A； PDBConstruct 1–519； UniProt 1–519 Author chain B； PDBConstruct 1–519； UniProt 1–519 Author chain G； PDBConstruct 1–519； UniProt 1–519 Author chain H； PDBConstruct 1–519； UniProt 1–519 Author chain M； PDBConstruct 1–519； UniProt 1–519 Author chain N； PDBConstruct 1–519； UniProt 1–519 Author chain P； PDBConstruct 1–519； UniProt 1–519 Author chain R； PDBConstruct 1–519； UniProt 1–519 Author chain S； PDBConstruct 1–519； UniProt 1–519 Author chain T； PDBConstruct 1–519； UniProt 1–519 Author chain V； PDBConstruct 1–519； UniProt 1–519 Author chain W； PDBConstruct 1–519； UniProt 1–519 Author chain X； PDBConstruct 1–519； UniProt 1–519 Author chain C； PDBConstruct 1–519； UniProt 1–519 Author chain D； PDBConstruct 1–519； UniProt 1–519 Author chain E； PDBConstruct 1–519； UniProt 1–519 Author chain F； PDBConstruct 1–519； UniProt 1–519 Author chain I； PDBConstruct 1–519； UniProt 1–519 Author chain J； PDBConstruct 1–519； UniProt 1–519 Author chain K； PDBConstruct 1–519； UniProt 1–519 Author chain L； PDBConstruct 1–519； UniProt 1–519 Author chain O； PDBConstruct 1–519； UniProt 1–519 Author chain Q； PDBConstruct 1–519； UniProt 1–519 Author chain U； PDBConstruct 1–519； UniProt 1–519

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	7v3x
Deposition date deposition_date	2021-08-11
Structure title title	Crystal Structure of Cyanobacterial Circadian Clock Protein KaiC
Keywords keywords	clock 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.

7v3x__assembly_2__model_1

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

Download this curve (.dat)

7v3x__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

7v3x__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	41.30 Å
Rg (electron density)	40.52 Å
Total Rg	40.86 Å
Atom count	21142
Residues	2807
Excluded volume	370440 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`7v3x__assembly_1__model_1`	hexameric （6）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`7v3x__assembly_2__model_1`	hexameric （6）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`7v3x__assembly_3__model_1`	hexameric （6）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`7v3x__assembly_4__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 (6)

Entity 1 Entity 1 polymer

Description description	Circadian clock protein kinase KaiC
Molecular weight formula_weight	58152.8 kDa
EC 编号 ec_number	2.7.11.1
Source method src_method	man
Copy count entity_count	13

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,G,H,N,R,M,P,T,X,S,V,W
Atom count atom_count	78739

MTSAEMTSPNNNSEHQAIAKMRTMIEGFDDISHGGLPIGRSTLVSGTSGTGKTLFSIQFLYNGIIEFDEPGVFVTFEETPQDIIKNARSFGWDLAKLVDEGKLFILDASPDPEGQEVVGGFDLSALIERINYAIQKYRARRVSIDSVTSVFQQYDASSVVRRELFRLVARLKQIGATTVMTTERIEEYGPIARYGVEEFVSDNVVILRNVLEGERRRRTLEILKLRGTSHMKGEYPFTITDHGINIFPLGAMRLTQRSSNVRVSSGVVRLDEMCGGGFFKDSIILATGATGTGKTLLVSRFVENACANKERAILFAYEESRAQLLRNAYSWGMDFEEMERQNLLKIVCAYPESAGLEDHLQIIKSEINDFKPARIAIDSLSALARGVSNNAFRQFVIGVTGYAKQEEITGLFTNTSDQFMGAHSITDSHISTITDTIILLQYVEIRGEMSRAINVFKMRGSWHDKAIREFMISDKGPDIKDSFRNFERIISGSPTRITVDEKSELSRIVRGVQEKGPES

Source Source

Source organism organism	Synechococcus elongatus (strain PCC 7942 / FACHB-805)
Common name common_name	Anacystis nidulans R2
NCBI taxonomy ID ncbi_taxonomy_id	1140
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 polymer

Description description	Circadian clock protein kinase KaiC
Molecular weight formula_weight	58232.7 kDa
EC 编号 ec_number	2.7.11.1
Source method src_method	man
Copy count entity_count	11

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E,F,C,D,K,L,I,J,O,Q,U

Source Source

Source organism organism	Synechococcus elongatus (strain PCC 7942 / FACHB-805)
Common name common_name	Anacystis nidulans R2
NCBI taxonomy ID ncbi_taxonomy_id	1140
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 3 Entity 3 non-polymer

Description description	ADENOSINE-5'-TRIPHOSPHATE
Molecular weight formula_weight	507.2 kDa
Source method src_method	syn
Copy count entity_count	45

Entity 4 Entity 4 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	36

Entity 5 Entity 5 non-polymer

Description description	ADENOSINE-5'-DIPHOSPHATE
Molecular weight formula_weight	427.2 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	92

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6. Fold Classification (SCOP + CATH) 47 domains

CATH v4.4 (47 domains)

Domain ID domain_id	7v3xA01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	7v3xA02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	7v3xB01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	7v3xB02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	7v3xC01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	7v3xC02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	7v3xD01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	7v3xD02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	7v3xE01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	7v3xE02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	7v3xF01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	7v3xF02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	7v3xG01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	7v3xG02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	7v3xH01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	7v3xH02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	7v3xI01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	7v3xI02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	7v3xJ01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	7v3xJ02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	7v3xK01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	7v3xK02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	7v3xL01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	7v3xL02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	7v3xM01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	7v3xM02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	7v3xN01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	7v3xN02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	7v3xO01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	7v3xO02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	7v3xP01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	7v3xP02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	7v3xQ01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	7v3xQ02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	7v3xR01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	7v3xR02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	7v3xS01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	7v3xS02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	7v3xT01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	7v3xT02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	7v3xU01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	7v3xU02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	7v3xV01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	7v3xW01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	7v3xW02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	7v3xX01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	7v3xX02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

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Unit-cell length a length_a	185.492 Å
Unit-cell length b length_b	205.803 Å
Unit-cell length c length_c	186.177 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	115.14 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	26

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

Resolution resolution	3.100 Å
Low-resolution limit resolution_low	49.220 Å
R factor r_factor	0.2777
R_work r_work	0.2745
R_free r_free	0.3397

Crystal Structure of Cyanobacterial Circadian Clock Protein KaiC

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

Circadian clock protein kinase KaiC

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

7v3x__assembly_2__model_1

7v3x__assembly_2__model_1 | I(q)

7v3x__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 (6)

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 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 47 domains

CATH v4.4 (47 domains)

7. Citations (1)

Crystal Structure of Cyanobacterial Circadian Clock Protein KaiC

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

Circadian clock protein kinase KaiC

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

7v3x__assembly_2__model_1

7v3x__assembly_2__model_1 | I(q)

7v3x__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 (6)

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 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 47 domains

CATH v4.4 (47 domains)

7. Citations (1)