SAXSdb — 1ygb

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

Alanyl-tRNA synthetase

Aquifex aeolicus

State in the Current Structure

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

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SYA_AQUAE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–454； UniProt 1–454

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	1ygb
Deposition date deposition_date	2005-01-04
Structure title title	Crystal Structure of the catalytic fragment of alanyl-tRNA synthetase in complex with L-serine
Keywords keywords	helix-turn-helix motif, alpha-beta fold, amino acid 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.

1ygb__assembly_1__model_1

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

Download this curve (.dat)

1ygb__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1ygb__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	24.85 Å
Rg (electron density)	23.84 Å
Total Rg	24.69 Å
Atom count	3648
Residues	448
Excluded volume	65079 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1ygb__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1ygb__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	Alanyl-tRNA synthetase
Molecular weight formula_weight	53772.2 kDa
EC 编号 ec_number	6.1.1.7
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	3794

MSLSAHEIRELFLSFFEKKGHTRVKSAPLVPENDPTLLFVNAGMVPFKNVFLGLEKRPYKRATSCQKCLRVSGKHNDLEQVGYTSRHHTFFEMLGNFSFGDYFKKEAIEYAWEFVTEVLKLPKEKLYVSVYKDDEEAYRIWNEHIGIPSERIWRLGEEDNFWQMGDVGPCGPSSEIYVDRGEEYEGDERYLEIWNLVFMQYNRDENGVLTPLPHPNIDTGMGLERIASVLQGKNSNFEIDIIFPLIQFGEEVSGKKYGEKFETDVALRVIADHLRAITFAISDGVIPSNEGRGYVIRRILRRAMRFGYKLGIENPFLYKGVDLVVDIMKEPYPELELSREFVKGIVKGEEKRFIKTLKAGMEYIQEVIQKALEEGRKTLSGKEVFTAYDTYGFPVDLIDEIAREKGLGIDLEGFQCELEEQRERARKHFKVEAKKVKPVYSHLKELGKTSAFVGAAALEHHHHHH

Source Source

Source organism organism	Aquifex aeolicus
NCBI taxonomy ID ncbi_taxonomy_id	63363
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	SERINE
Molecular weight formula_weight	105.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	146

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6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d1ygba1
Class class	a — All alpha proteins
Fold Fold fold	a.203 — Putative anticodon-binding domain of alanyl-tRNA synthetase (AlaRS)
Superfamily Superfamily superfamily	a.203.1 — Putative anticodon-binding domain of alanyl-tRNA synthetase (AlaRS)
Family Family family	a.203.1.1 — Putative anticodon-binding domain of alanyl-tRNA synthetase (AlaRS)

Domain ID domain_id	d1ygba2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.104 — Class II aaRS and biotin synthetases
Superfamily Superfamily superfamily	d.104.1 — Class II aaRS and biotin synthetases
Family Family family	d.104.1.1 — Class II aminoacyl-tRNA synthetase (aaRS)-like, catalytic domain

Domain ID domain_id	d1ygba3
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

CATH v4.4 (1 domains)

Domain ID domain_id	1ygbA01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	930 — BirA Bifunctional Protein; domain 2
Homologous superfamily homologous superfamily	10 — Bira Bifunctional Protein; Domain 2

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Unit-cell length a length_a	74.091 Å
Unit-cell length b length_b	74.091 Å
Unit-cell length c length_c	173.595 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	8

Space group space_group	P 41 21 2
Space-group number int_tables_number	92
Crystal system crystal_system	—

Resolution resolution	2.480 Å
Low-resolution limit resolution_low	50.000 Å
R factor r_factor	0.2100
R_work r_work	0.1990
R_free r_free	0.2320

Crystal Structure of the catalytic fragment of alanyl-tRNA synthetase in complex with L-serine

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

Alanyl-tRNA 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

1ygb__assembly_1__model_1

1ygb__assembly_1__model_1 | I(q)

1ygb__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) 4 domains

SCOP 2.08 (3 domains)

CATH v4.4 (1 domains)

7. Citations (2)

Crystal Structure of the catalytic fragment of alanyl-tRNA synthetase in complex with L-serine

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

Alanyl-tRNA 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

1ygb__assembly_1__model_1

1ygb__assembly_1__model_1 | I(q)

1ygb__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) 4 domains

SCOP 2.08 (3 domains)

CATH v4.4 (1 domains)

7. Citations (2)