SAXSdb — 4gvz

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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	ADENOSINE-5'-DIPHOSPHATE × 1 MAGNESIUM ION × 1 NITRATE ION × 1 D-ARGININE × 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

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	4gvz
Deposition date deposition_date	2012-08-31
Structure title title	Crystal structure of arginine kinase in complex with D-arginine, MgADP, and nitrate.
Keywords keywords	Arginine kinase, Phosphagen kinase, Transferase, Transition state analog, Kinase; 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.

4gvz__assembly_1__model_1

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

Download this curve (.dat)

4gvz__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4gvz__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	20.68 Å
Rg (electron density)	19.98 Å
Total Rg	20.92 Å
Atom count	2861
Residues	356
Excluded volume	50706 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4gvz__assembly_1__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 (6)

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	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	2977

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	ADENOSINE-5'-DIPHOSPHATE
Molecular weight formula_weight	427.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	NITRATE ION
Molecular weight formula_weight	62.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 non-polymer

Description description	D-ARGININE
Molecular weight formula_weight	175.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	85

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6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d4gvza1
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	d4gvza2
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 (2 domains)

Domain ID domain_id	4gvzA01
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	4gvzA02
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	64.109 Å
Unit-cell length b length_b	65.382 Å
Unit-cell length c length_c	85.912 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	4

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.960 Å
Low-resolution limit resolution_low	35.900 Å
R factor r_factor	0.1940
R_work r_work	0.1920
R_free r_free	0.2290

Crystal structure of arginine kinase in complex with D-arginine, MgADP, and nitrate.

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

4gvz__assembly_1__model_1

4gvz__assembly_1__model_1 | I(q)

4gvz__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 (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

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) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)

Crystal structure of arginine kinase in complex with D-arginine, MgADP, and nitrate.

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

4gvz__assembly_1__model_1

4gvz__assembly_1__model_1 | I(q)

4gvz__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 (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

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) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)