6u1c

Apo form of Thermus thermophilus D-alanine-D-alanine ligase

Method: X-RAY DIFFRACTION

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

D-alanine--D-alanine ligase

Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)

State in the Current Structure

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

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	DDL_THET8
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–321； UniProt 1–319 Author chain B； PDBConstruct 3–321； UniProt 1–319 Author chain C； PDBConstruct 3–321； UniProt 1–319 Author chain D； PDBConstruct 3–321； UniProt 1–319

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	6u1c
Deposition date deposition_date	2019-08-15
Structure title title	Apo form of Thermus thermophilus D-alanine-D-alanine ligase
Keywords keywords	ATP-grasp domain, ATP binding, metal binding, LIGASE; 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.

6u1c__assembly_2__model_1

Assembly 2 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

6u1c__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6u1c__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	25.04 Å
Rg (electron density)	24.02 Å
Total Rg	24.91 Å
Atom count	4417
Residues	601
Excluded volume	79578 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6u1c__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`6u1c__assembly_2__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 (2)

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6. Fold Classification (SCOP + CATH) 20 domains

SCOP 2.08 (12 domains)

Domain ID domain_id	d6u1ca1
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.30.1.0 — automated matches

Domain ID domain_id	d6u1ca2
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.142.1.0 — automated matches

Domain ID domain_id	d6u1ca3
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d6u1ca4
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d6u1cb1
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.30.1.0 — automated matches

Domain ID domain_id	d6u1cb2
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.142.1.0 — automated matches

Domain ID domain_id	d6u1cc1
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.30.1.0 — automated matches

Domain ID domain_id	d6u1cc2
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.142.1.0 — automated matches

Domain ID domain_id	d6u1cc3
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d6u1cc4
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d6u1cd1
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.30.1.0 — automated matches

Domain ID domain_id	d6u1cd2
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.142.1.0 — automated matches

CATH v4.4 (8 domains)

Domain ID domain_id	6u1cA01
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	6u1cB01
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	6u1cB02
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	6u1cB03
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	6u1cC01
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	6u1cC02
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	6u1cD01
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	6u1cD02
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

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Unit-cell length a length_a	55.866 Å
Unit-cell length b length_b	68.688 Å
Unit-cell length c length_c	91.789 Å
Unit-cell angle α angle_alpha	68.31 °
Unit-cell angle β angle_beta	79.71 °
Unit-cell angle γ angle_gamma	65.99 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Resolution resolution	2.200 Å
Low-resolution limit resolution_low	33.253 Å
R factor r_factor	0.2395
R_work r_work	0.2380
R_free r_free	0.2652

Description description	D-alanine--D-alanine ligase
Molecular weight formula_weight	35789.0 kDa
EC 编号 ec_number	6.3.2.4
Source method src_method	man
Copy count entity_count	4

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	9078

Apo form of Thermus thermophilus D-alanine-D-alanine ligase

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

D-alanine--D-alanine ligase

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

6u1c__assembly_2__model_1

6u1c__assembly_2__model_1 | I(q)

6u1c__assembly_2__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 water

6. Fold Classification (SCOP + CATH) 20 domains

SCOP 2.08 (12 domains)

CATH v4.4 (8 domains)

7. Citations (1)

Source organism organism	Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
NCBI taxonomy ID ncbi_taxonomy_id	300852
Host organism host_organism	Escherichia coli BL21(DE3)

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	164

Apo form of Thermus thermophilus D-alanine-D-alanine ligase

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

D-alanine--D-alanine ligase

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

6u1c__assembly_2__model_1

6u1c__assembly_2__model_1 | I(q)

6u1c__assembly_2__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 water

6. Fold Classification (SCOP + CATH) 20 domains

SCOP 2.08 (12 domains)

CATH v4.4 (8 domains)

7. Citations (1)