SAXSdb — 5c5e

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

Circadian clock protein KaiA

Synechococcus elongatus (strain PCC 7942)

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	KaiC C-terminal peptide × 2 2-(6-hydroxy-3-oxo-3H-xanthen-9-yl)-5-[(sulfanylcarbonyl)amino]benzoic acid × 2 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	KAIA_SYNE7
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–284； UniProt 1–284 Author chain B； PDBConstruct 1–284； UniProt 1–284

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	5c5e
Deposition date deposition_date	2015-06-19
Structure title title	Structure of KaiA dimer in complex with C-terminal KaiC peptide at 2.8 A resolution
Keywords keywords	Clock protein KaiA-KaiC complex, TRANSCRIPTION; TRANSCRIPTION
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.

5c5e__assembly_1__model_1

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

Download this curve (.dat)

5c5e__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5c5e__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	28.22 Å
Rg (electron density)	27.13 Å
Total Rg	27.96 Å
Atom count	4920
Residues	604
Excluded volume	87239 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5c5e__assembly_1__model_1`	tetrameric （4）	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	Circadian clock protein KaiA
Molecular weight formula_weight	33495.1 kDa
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	5018

MLSQIAICIWVESTAILQDCQRALSADRYQLQVCESGEMLLEYAQTHRDQIDCLILVAANPSFRAVVQQLCFEGVVVPAIVVGDRDSEDPDEPAKEQLYHSAELHLGIHQLEQLPYQVDAALAEFLRLAPVETMADHIMLMGANHDPELSSQQRDLAQRLQERLGYLGVYYKRDPDRFLRNLPAYESQKLHQAMQTSYREIVLSYFSPNSNLNQSIDNFVNMAFFADVPVTKVVEIHMELMDEFAKKLRVEGRSEDILLDYRLTLIDVIAHLCEMYRRSIPRETHHHHHH

Source Source

Source organism organism	Synechococcus elongatus (strain PCC 7942)
NCBI taxonomy ID ncbi_taxonomy_id	1140
Host organism host_organism	ESCHERICHIA COLI

Entity 2 Entity 2 polymer

Description description	KaiC C-terminal peptide
Molecular weight formula_weight	2247.5 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	G,H

DEKSELSRIVRGVQEKGPES

Entity 3 Entity 3 non-polymer

Description description	2-(6-hydroxy-3-oxo-3H-xanthen-9-yl)-5-[(sulfanylcarbonyl)amino]benzoic acid
Molecular weight formula_weight	407.4 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	98

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6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	5c5eA01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	2300 — Response regulator

Domain ID domain_id	5c5eA02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1240 — Methyltransferase, Methionine Synthase (B12-binding Domains); Chain A, domain 1
Homologous superfamily homologous superfamily	30 — KaiA/RbsU domain

Domain ID domain_id	5c5eB01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	2300 — Response regulator

Domain ID domain_id	5c5eB02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1240 — Methyltransferase, Methionine Synthase (B12-binding Domains); Chain A, domain 1
Homologous superfamily homologous superfamily	30 — KaiA/RbsU domain

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Unit-cell length a length_a	97.430 Å
Unit-cell length b length_b	97.430 Å
Unit-cell length c length_c	124.520 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	16

Space group space_group	P 43 21 2
Space-group number int_tables_number	96
Crystal system crystal_system	—

Resolution resolution	2.820 Å
Low-resolution limit resolution_low	46.192 Å
R factor r_factor	0.2430
R_work r_work	0.2397
R_free r_free	0.3029

Structure of KaiA dimer in complex with C-terminal KaiC peptide at 2.8 A resolution

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

Circadian clock protein KaiA

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

5c5e__assembly_1__model_1

5c5e__assembly_1__model_1 | I(q)

5c5e__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) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)

Structure of KaiA dimer in complex with C-terminal KaiC peptide at 2.8 A resolution

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

Circadian clock protein KaiA

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

5c5e__assembly_1__model_1

5c5e__assembly_1__model_1 | I(q)

5c5e__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) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)