2yzm

Structure of D-Alanine:D-Alanine Ligase with substrate from Thermus thermophilus HB8

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

State in the Current Structure

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

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q5SHZ3_THET8
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–319； UniProt 1–319 Author chain B； PDBConstruct 1–319； UniProt 1–319 Author chain C； PDBConstruct 1–319； 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	2yzm
Deposition date deposition_date	2007-05-06
Structure title title	Structure of D-Alanine:D-Alanine Ligase with substrate from Thermus thermophilus HB8
Keywords keywords	;D-Alanine:D-Alanine Ligase, Cell shape, Peptidoglycan synthesis, Structural Genomics, NPPSFA, National Project on Protein Structural and Functional Analyses, RIKEN Structural Genomics/Proteomics Initiative, RSGI, 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.

2yzm__assembly_1__model_1

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

Download this curve (.dat)

2yzm__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2yzm__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	26.57 Å
Rg (electron density)	25.52 Å
Total Rg	26.33 Å
Atom count	4849
Residues	631
Excluded volume	87322 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2yzm__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2yzm__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 (3)

Entity 1 Entity 1 polymer

Description description	D-alanine--D-alanine ligase
Molecular weight formula_weight	34699.8 kDa
EC 编号 ec_number	6.3.2.4
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C
Atom count atom_count	7476

MRVLLIAGGVSPEHEVSLLSAEGVLRHIPFPTDLAVIAQDGRWLLGEKALTALEAKAAPEGEHPFPPPLSWERYDVVFPLLHGRFGEDGTVQGFLELLGKPYVGAGVAASALCMDKDLSKRVLAQAGVPVVPWVAVRKGEPPVVPFDPPFFVKPANTGSSVGISRVERFQDLEAALALAFRYDEKAVVEKALSPVRELEVGVLGNVFGEASPVGEVRYEAPFYDYETKYTPGRAELLIPAPLDPGTQETVQELALKAYKVLGVRGMARVDFFLAEGELYLNELNTIPGFTPTSMYPRLFEAGGVAYPELLRRLVELALT

Source Source

Source organism organism	Thermus thermophilus
NCBI taxonomy ID ncbi_taxonomy_id	300852
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	D-ALANINE
Molecular weight formula_weight	89.1 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	266

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6. Fold Classification (SCOP + CATH) 15 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d2yzma1
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	d2yzma2
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	d2yzmb1
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	d2yzmb2
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	d2yzmc1
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	d2yzmc2
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 (9 domains)

Domain ID domain_id	2yzmA01
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	2yzmA02
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	2yzmA03
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	2yzmB01
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	2yzmB02
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	2yzmB03
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	2yzmC01
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	2yzmC02
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	2yzmC03
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	166.705 Å
Unit-cell length b length_b	55.849 Å
Unit-cell length c length_c	141.387 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	109.34 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	12

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

Resolution resolution	2.210 Å
Low-resolution limit resolution_low	44.160 Å
R factor r_factor	0.2240
R_work r_work	0.2240
R_free r_free	0.2660

Structure of D-Alanine:D-Alanine Ligase with substrate from Thermus thermophilus HB8

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

2yzm__assembly_1__model_1

2yzm__assembly_1__model_1 | I(q)

2yzm__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) 15 domains

SCOP 2.08 (6 domains)

CATH v4.4 (9 domains)

7. Citations (1)

Structure of D-Alanine:D-Alanine Ligase with substrate from Thermus thermophilus HB8

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

2yzm__assembly_1__model_1

2yzm__assembly_1__model_1 | I(q)

2yzm__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) 15 domains

SCOP 2.08 (6 domains)

CATH v4.4 (9 domains)

7. Citations (1)