SAXSdb — 1uc9

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

lysine biosynthesis enzyme

Thermus thermophilus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	ADENOSINE-5'-DIPHOSPHATE × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q84BR0_THETH
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–280； UniProt 1–280 Author chain B； PDBConstruct 1–280； UniProt 1–280

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	1uc9
Deposition date deposition_date	2003-04-09
Structure title title	Crystal structure of a lysine biosynthesis enzyme, Lysx, from thermus thermophilus HB8
Keywords keywords	;LYSINE BIOSYNTHESIS, ALPHA-AMINOADIPATE PATHWAY, RIKEN Structural Genomics/Proteomics Initiative, RSGI, Structural Genomics, biosynthetic protein ;; BIOSYNTHETIC PROTEIN
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.

1uc9__assembly_1__model_1

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

Download this curve (.dat)

1uc9__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1uc9__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	25.56 Å
Rg (electron density)	24.56 Å
Total Rg	25.40 Å
Atom count	3912
Residues	509
Excluded volume	69955 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1uc9__assembly_1__model_1`	dimeric （2）	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	lysine biosynthesis enzyme
Molecular weight formula_weight	30425.2 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	3970

MLAILYDRIRPDERMLFERAEALGLPYKKVYVPALPMVLGERPKELEGVTVALERCVSQSRGLAAARYLTALGIPVVNRPEVIEACGDKWATSVALAKAGLPQPKTALATDREEALRLMEAFGYPVVLKPVIGSWGRLXXXXXXXXXXXXXXXXKEVLGGFQHQLFYIQEYVEKPGRDIRVFVVGERAIAAIYRRSAHWITNTARGGQAENCPLTEEVARLSVKAAEAVGGGVVAVDLFESERGLLVNEVNHTMEFKNSVHTTGVDIPGEILKYAWSLAS

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	ADENOSINE-5'-DIPHOSPHATE
Molecular weight formula_weight	427.2 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	58

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6. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d1uc9a1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.30 — PreATP-grasp domain
Superfamily Superfamily superfamily	c.30.1 — PreATP-grasp domain
Family Family family	c.30.1.6 — Lysine biosynthesis enzyme LysX, N-terminal domain

Domain ID domain_id	d1uc9a2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.142 — ATP-grasp
Superfamily Superfamily superfamily	d.142.1 — Glutathione synthetase ATP-binding domain-like
Family Family family	d.142.1.7 — Lysine biosynthesis enzyme LysX ATP-binding domain

Domain ID domain_id	d1uc9b1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.30 — PreATP-grasp domain
Superfamily Superfamily superfamily	c.30.1 — PreATP-grasp domain
Family Family family	c.30.1.6 — Lysine biosynthesis enzyme LysX, N-terminal domain

Domain ID domain_id	d1uc9b2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.142 — ATP-grasp
Superfamily Superfamily superfamily	d.142.1 — Glutathione synthetase ATP-binding domain-like
Family Family family	d.142.1.7 — Lysine biosynthesis enzyme LysX ATP-binding domain

CATH v4.4 (6 domains)

Domain ID domain_id	1uc9A01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	1uc9A02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1490 — Dna Ligase; domain 1
Homologous superfamily homologous superfamily	20 — ATP-grasp fold, A domain

Domain ID domain_id	1uc9A03
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	470 — D-amino Acid Aminotransferase; Chain A, domain 1
Homologous superfamily homologous superfamily	20 — ATP-grasp fold, B domain

Domain ID domain_id	1uc9B01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	1uc9B02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1490 — Dna Ligase; domain 1
Homologous superfamily homologous superfamily	20 — ATP-grasp fold, A domain

Domain ID domain_id	1uc9B03
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	470 — D-amino Acid Aminotransferase; Chain A, domain 1
Homologous superfamily homologous superfamily	20 — ATP-grasp fold, B domain

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Unit-cell length a length_a	126.591 Å
Unit-cell length b length_b	52.145 Å
Unit-cell length c length_c	105.105 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	123.24 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	2.380 Å
Low-resolution limit resolution_low	49.800 Å
R factor r_factor	—
R_work r_work	0.2430
R_free r_free	0.2803

Crystal structure of a lysine biosynthesis enzyme, Lysx, from thermus thermophilus HB8

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

lysine biosynthesis enzyme

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

1uc9__assembly_1__model_1

1uc9__assembly_1__model_1 | I(q)

1uc9__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) 10 domains

SCOP 2.08 (4 domains)

CATH v4.4 (6 domains)

7. Citations (1)

Crystal structure of a lysine biosynthesis enzyme, Lysx, from thermus thermophilus HB8

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

lysine biosynthesis enzyme

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

1uc9__assembly_1__model_1

1uc9__assembly_1__model_1 | I(q)

1uc9__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) 10 domains

SCOP 2.08 (4 domains)

CATH v4.4 (6 domains)

7. Citations (1)