SAXSdb — 2zzg

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

Alanyl-tRNA synthetase

Pyrococcus horikoshii

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	ZINC ION × 2 '5'-O-(N-(L-ALANYL)-SULFAMOYL)ADENOSINE × 1 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	ZINC ION × 2 '5'-O-(N-(L-ALANYL)-SULFAMOYL)ADENOSINE × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SYA_PYRHO
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–752； UniProt 1–752 Author chain B； PDBConstruct 1–752； UniProt 1–752

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	2zzg
Deposition date deposition_date	2009-02-10
Structure title title	Crystal structure of alanyl-tRNA synthetase in complex with 5''-O-(N-(L-alanyl)-sulfamyoxyl) adenine without oligomerization domain
Keywords keywords	ligase, hydrolase; 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.

2zzg__assembly_1__model_1

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

Download this curve (.dat)

2zzg__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2zzg__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	30.16 Å
Rg (electron density)	29.51 Å
Total Rg	30.31 Å
Atom count	6034
Residues	738
Excluded volume	108510 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2zzg__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2zzg__assembly_2__model_1`	monomeric （1）	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 (4)

Entity 1 Entity 1 polymer

Description description	Alanyl-tRNA synthetase
Molecular weight formula_weight	86859.7 kDa
EC 编号 ec_number	6.1.1.7
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	12055

MEFIMKTRMFEEEGWIRKKCKVCGKPFWTLDPDRETCGDPPCDEYQFIGKPGIPRKYTLDEMREKFLRFFEKHEIYPHGRVKRYPVLPRWRDDVLLVGASIMDFQPWVISGEADPPANPLVISQPSIRFTDIDNVGITGRHFTIFEMMAHHAFNYPGKPIYWMDETVELAFEFFTKELKMKPEDITFKENPWAGGGNAGPAFEVLYRGLEVATLVFMQYKKAPENAPQDQVVVIKGEKYIPMETKVVDTGYGLERLVWMSQGTPTAYDAVLGYVVEPLKKMAGIEKIDEKILMENSRLAGMFDIEDLGDLRYLREQVAKRVGITVEELEKAIRPYELIYAIADHTKALTFMLADGVVPSNVKAGYLARLLIRKSIRHLRELGLEVPLSEIVALHIKELHKTFPEFKEMEDIILEMIELEEKKYAETLRRGSDLVRREIAKLKKKGIKEIPVEKLVTFYESHGLTPEIVKEIAEKEGVKVNIPDNFYSMVAKEAERTKEEKGEELVDFELLKDLPDTRRLYYEDPFMKEFDAKVLRVIKDWVILDATAFYPEGGGQPYDTGVLIVNGREVKVTNVQKVGKVIIHKVEDPGAFKEGMIVHGKIDWKRRIQHMRHHTGTHVLMGALVRVLGRHVWQAGSQLTTDWARLDISHYKRISEEELKEIEMLANRIVMEDRKVTWEWLPRTTAEQKYGFRLYQGGVVPGREIRVVKIEDWDVQACGGTHLPSTGLVGPIKILRTERIQDGVERIIFACGE

Source Source

Source organism organism	Pyrococcus horikoshii
NCBI taxonomy ID ncbi_taxonomy_id	53953
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 non-polymer

Description description	'5'-O-(N-(L-ALANYL)-SULFAMOYL)ADENOSINE
Molecular weight formula_weight	417.4 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	2

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6. Fold Classification (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

Domain ID domain_id	2zzgA01
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

Domain ID domain_id	2zzgA03
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	30 — Elongation Factor Tu (Ef-tu); domain 3
Homologous superfamily homologous superfamily	130 —

Domain ID domain_id	2zzgA04
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	980 — Threonyl-tRNA Synthetase; Chain A, domain 2
Homologous superfamily homologous superfamily	10 — Threonyl-trna Synthetase; Chain A, domain 2

Domain ID domain_id	2zzgA05
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	54 — Replication Terminator Protein; Chain A, domain 2
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	2zzgB01
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

Domain ID domain_id	2zzgB03
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	30 — Elongation Factor Tu (Ef-tu); domain 3
Homologous superfamily homologous superfamily	130 —

Domain ID domain_id	2zzgB04
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	980 — Threonyl-tRNA Synthetase; Chain A, domain 2
Homologous superfamily homologous superfamily	10 — Threonyl-trna Synthetase; Chain A, domain 2

Domain ID domain_id	2zzgB05
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	54 — Replication Terminator Protein; Chain A, domain 2
Homologous superfamily homologous superfamily	20 —

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Unit-cell length a length_a	70.874 Å
Unit-cell length b length_b	89.205 Å
Unit-cell length c length_c	94.905 Å
Unit-cell angle α angle_alpha	117.31 °
Unit-cell angle β angle_beta	90.40 °
Unit-cell angle γ angle_gamma	107.36 °
Molecules per unit cell Z z_pdb	2

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

Resolution resolution	3.100 Å
Low-resolution limit resolution_low	50.000 Å
R factor r_factor	0.2031
R_work r_work	0.1994
R_free r_free	0.2721

Crystal structure of alanyl-tRNA synthetase in complex with 5''-O-(N-(L-alanyl)-sulfamyoxyl) adenine without oligomerization domain

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

2zzg__assembly_1__model_1

2zzg__assembly_1__model_1 | I(q)

2zzg__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 (4)

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 water

6. Fold Classification (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

7. Citations (1)

Crystal structure of alanyl-tRNA synthetase in complex with 5''-O-(N-(L-alanyl)-sulfamyoxyl) adenine without oligomerization domain

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

2zzg__assembly_1__model_1

2zzg__assembly_1__model_1 | I(q)

2zzg__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 (4)

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 water

6. Fold Classification (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

7. Citations (1)