1kh3

Crystal Structure of Thermus thermophilus HB8 Argininosuccinate Synthetase in complex with inhibitor

Method: X-RAY DIFFRACTION

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

Argininosuccinate Synthetase

Thermus thermophilus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 4	SULFATE ION × 4 MAGNESIUM ION × 4 PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 4 ARGININE × 4 ASPARTIC ACID × 4 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	ASSY_THET8
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–400； UniProt 1–400 Author chain B； PDBConstruct 1–400； UniProt 1–400 Author chain C； PDBConstruct 1–400； UniProt 1–400 Author chain D； PDBConstruct 1–400； UniProt 1–400

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	1kh3
Deposition date deposition_date	2001-11-29
Structure title title	Crystal Structure of Thermus thermophilus HB8 Argininosuccinate Synthetase in complex with inhibitor
Keywords keywords	ligase, RIKEN Structural Genomics/Proteomics Initiative, RSGI, Structural Genomics; LIGASE
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.

1kh3__assembly_1__model_1

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

Download this curve (.dat)

1kh3__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1kh3__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	34.87 Å
Rg (electron density)	34.01 Å
Total Rg	34.67 Å
Atom count	12447
Residues	1538
Excluded volume	221010 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1kh3__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 (7)

Entity 1 Entity 1 polymer

Description description	Argininosuccinate Synthetase
Molecular weight formula_weight	44876.0 kDa
EC 编号 ec_number	6.3.4.5
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	13014

MKIVLAYSGGLDTSIILKWLKETYRAEVIAFTADIGQGEEVEEAREKALRTGASKAIALDLKEEFVRDFVFPMMRAGAVYEGYYLLGTSIARPLIAKHLVRIAEEEGAEAIAHGATGKGNDQVRFELTAYALKPDIKVIAPWREWSFQGRKEMIAYAEAHGIPVPVTQEKPYSMDANLLHISYEGGVLEDPWAEPPKGMFRMTQDPEEAPDAPEYVEVEFFEGDPVAVNGERLSPAALLQRLNEIGGRHGVGRVDIVENRFVGMKSRGVYETPGGTILYHARRAVESLTLDREVLHQRDMLSPKYAELVYYGFWYAPEREALQAYFDHVARSVTGVARLKLYKGNVYVVGRKAPKSLYRQDLVSFDEAGGYDQKDAEGFIKIQALRLRVRALVEREGHGA

Source Source

Source organism organism	Thermus thermophilus
NCBI taxonomy ID ncbi_taxonomy_id	274
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	4

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	4

Entity 4 Entity 4 non-polymer

Description description	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
Molecular weight formula_weight	506.2 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 5 Entity 5 non-polymer

Description description	ARGININE
Molecular weight formula_weight	175.2 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 6 Entity 6 non-polymer

Description description	ASPARTIC ACID
Molecular weight formula_weight	133.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 7 Entity 7 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	567

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6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

Domain ID domain_id	d1kh3a1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.26 — Adenine nucleotide alpha hydrolase-like
Superfamily Superfamily superfamily	c.26.2 — Adenine nucleotide alpha hydrolases-like
Family Family family	c.26.2.1 — N-type ATP pyrophosphatases

Domain ID domain_id	d1kh3a2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.210 — Argininosuccinate synthetase, C-terminal domain
Superfamily Superfamily superfamily	d.210.1 — Argininosuccinate synthetase, C-terminal domain
Family Family family	d.210.1.1 — Argininosuccinate synthetase, C-terminal domain

Domain ID domain_id	d1kh3b1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.26 — Adenine nucleotide alpha hydrolase-like
Superfamily Superfamily superfamily	c.26.2 — Adenine nucleotide alpha hydrolases-like
Family Family family	c.26.2.1 — N-type ATP pyrophosphatases

Domain ID domain_id	d1kh3b2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.210 — Argininosuccinate synthetase, C-terminal domain
Superfamily Superfamily superfamily	d.210.1 — Argininosuccinate synthetase, C-terminal domain
Family Family family	d.210.1.1 — Argininosuccinate synthetase, C-terminal domain

Domain ID domain_id	d1kh3c1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.26 — Adenine nucleotide alpha hydrolase-like
Superfamily Superfamily superfamily	c.26.2 — Adenine nucleotide alpha hydrolases-like
Family Family family	c.26.2.1 — N-type ATP pyrophosphatases

Domain ID domain_id	d1kh3c2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.210 — Argininosuccinate synthetase, C-terminal domain
Superfamily Superfamily superfamily	d.210.1 — Argininosuccinate synthetase, C-terminal domain
Family Family family	d.210.1.1 — Argininosuccinate synthetase, C-terminal domain

Domain ID domain_id	d1kh3d1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.26 — Adenine nucleotide alpha hydrolase-like
Superfamily Superfamily superfamily	c.26.2 — Adenine nucleotide alpha hydrolases-like
Family Family family	c.26.2.1 — N-type ATP pyrophosphatases

Domain ID domain_id	d1kh3d2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.210 — Argininosuccinate synthetase, C-terminal domain
Superfamily Superfamily superfamily	d.210.1 — Argininosuccinate synthetase, C-terminal domain
Family Family family	d.210.1.1 — Argininosuccinate synthetase, C-terminal domain

CATH v4.4 (8 domains)

Domain ID domain_id	1kh3A01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	620 — HUPs

Domain ID domain_id	1kh3A02
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	1260 — Argininosuccinate synthetase, chain A, domain 2
Homologous superfamily homologous superfamily	10 — Argininosuccinate synthetase, chain A, domain 2

Domain ID domain_id	1kh3B01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	620 — HUPs

Domain ID domain_id	1kh3B02
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	1260 — Argininosuccinate synthetase, chain A, domain 2
Homologous superfamily homologous superfamily	10 — Argininosuccinate synthetase, chain A, domain 2

Domain ID domain_id	1kh3C01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	620 — HUPs

Domain ID domain_id	1kh3C02
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	1260 — Argininosuccinate synthetase, chain A, domain 2
Homologous superfamily homologous superfamily	10 — Argininosuccinate synthetase, chain A, domain 2

Domain ID domain_id	1kh3D01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	620 — HUPs

Domain ID domain_id	1kh3D02
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	1260 — Argininosuccinate synthetase, chain A, domain 2
Homologous superfamily homologous superfamily	10 — Argininosuccinate synthetase, chain A, domain 2

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Unit-cell length a length_a	229.100 Å
Unit-cell length b length_b	229.100 Å
Unit-cell length c length_c	160.600 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	36

Space group space_group	H 3
Space-group number int_tables_number	146
Crystal system crystal_system	—

Resolution resolution	2.150 Å
Low-resolution limit resolution_low	10.000 Å
R factor r_factor	—
R_work r_work	0.2260
R_free r_free	0.2560

Crystal Structure of Thermus thermophilus HB8 Argininosuccinate Synthetase in complex with inhibitor

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

Argininosuccinate Synthetase

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

1kh3__assembly_1__model_1

1kh3__assembly_1__model_1 | I(q)

1kh3__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 (7)

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 non-polymer

Entity 7 Entity 7 water

6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

CATH v4.4 (8 domains)

7. Citations (1)

Crystal Structure of Thermus thermophilus HB8 Argininosuccinate Synthetase in complex with inhibitor

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

Argininosuccinate Synthetase

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

1kh3__assembly_1__model_1

1kh3__assembly_1__model_1 | I(q)

1kh3__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 (7)

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 non-polymer

Entity 7 Entity 7 water

6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

CATH v4.4 (8 domains)

7. Citations (1)