SAXSdb — 3m10

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

Arginine kinase

Limulus polyphemus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	SULFATE ION × 1 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	SULFATE ION × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	KARG_LIMPO
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–357； UniProt 1–357 Author chain B； PDBConstruct 1–357； UniProt 1–357

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	3m10
Deposition date deposition_date	2010-03-03
Structure title title	Substrate-free form of Arginine Kinase
Keywords keywords	Alpha-beta, ATP-binding, Kinase, Nucleotide-binding, Guanidino kinase, Phosphagen kinase, 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.

3m10__assembly_1__model_1

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

Download this curve (.dat)

3m10__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3m10__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	21.89 Å
Rg (electron density)	21.12 Å
Total Rg	22.07 Å
Atom count	2750
Residues	347
Excluded volume	48984 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3m10__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3m10__assembly_2__model_1`	monomeric （1）	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 (3)

Entity 1 Entity 1 polymer

Description description	Arginine kinase
Molecular weight formula_weight	40249.8 kDa
EC 编号 ec_number	2.7.3.3
Mutation mutation	E103Q, D112G, G116A
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	6522

MVDQATLDKLEAGFKKLQEASDCKSLLKKHLTKDVFDSIKNKKTGMGATLLDVIQSGVENLDSGVGIYAPDAESYRTFGPLFDPIIDDYHGGFKLTDKHPPKQWGDINTLVGLDPAGQFIISTRVRCGRSLQGYPFNPCLTAEQYKEMEEKVSSTLSSMEDELKGTYYPLTGMSKATQQQLIDDHFLFKEGDRFLQTANACRYWPTGRGIFHNDAKTFLVWVNEEDHLRIISMQKGGDLKTVYKRLVTAVDNIESKLPFSHDDRFGFLTFCPTNLGTTMRASVHIQLPKLAKDRKVLEDIASKFNLQVRGTRGEHTESEGGVYDISNKRRLGLTEYQAVREMQDGILEMIKMEKAAA

Source Source

Source organism organism	Limulus polyphemus
Common name common_name	Atlantic horseshoe crab
NCBI taxonomy ID ncbi_taxonomy_id	6850
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	960

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6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d3m10a1
Class class	a — All alpha proteins
Fold Fold fold	a.83 — Guanido kinase N-terminal domain
Superfamily Superfamily superfamily	a.83.1 — Guanido kinase N-terminal domain
Family Family family	a.83.1.1 — Guanido kinase N-terminal domain

Domain ID domain_id	d3m10a2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.128 — Glutamine synthetase/guanido kinase
Superfamily Superfamily superfamily	d.128.1 — Glutamine synthetase/guanido kinase
Family Family family	d.128.1.2 — Guanido kinase catalytic domain

Domain ID domain_id	d3m10b1
Class class	a — All alpha proteins
Fold Fold fold	a.83 — Guanido kinase N-terminal domain
Superfamily Superfamily superfamily	a.83.1 — Guanido kinase N-terminal domain
Family Family family	a.83.1.1 — Guanido kinase N-terminal domain

Domain ID domain_id	d3m10b2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.128 — Glutamine synthetase/guanido kinase
Superfamily Superfamily superfamily	d.128.1 — Glutamine synthetase/guanido kinase
Family Family family	d.128.1.2 — Guanido kinase catalytic domain

CATH v4.4 (4 domains)

Domain ID domain_id	3m10A01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	135 — Transferase Creatine Kinase; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — ATP:guanido phosphotransferase, N-terminal domain

Domain ID domain_id	3m10A02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	590 — Creatine Kinase; Chain A, domain 2
Homologous superfamily homologous superfamily	10 — Glutamine synthetase/guanido kinase, catalytic domain

Domain ID domain_id	3m10B01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	135 — Transferase Creatine Kinase; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — ATP:guanido phosphotransferase, N-terminal domain

Domain ID domain_id	3m10B02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	590 — Creatine Kinase; Chain A, domain 2
Homologous superfamily homologous superfamily	10 — Glutamine synthetase/guanido kinase, catalytic domain

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Unit-cell length a length_a	60.218 Å
Unit-cell length b length_b	90.428 Å
Unit-cell length c length_c	70.554 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	111.02 °
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	1.727 Å
Low-resolution limit resolution_low	26.618 Å
R factor r_factor	0.1918
R_work r_work	0.1903
R_free r_free	0.2423

Substrate-free form of Arginine Kinase

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

Arginine kinase

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

3m10__assembly_1__model_1

3m10__assembly_1__model_1 | I(q)

3m10__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (3)

Substrate-free form of Arginine Kinase

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

Arginine 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

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

3m10__assembly_1__model_1

3m10__assembly_1__model_1 | I(q)

3m10__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (3)