1irx

Crystal structure of class I lysyl-tRNA synthetase

Method: X-RAY DIFFRACTION

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

lysyl-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 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	ZINC ION × 2 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SYK_PYRHO
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–523； UniProt 1–523 Author chain B； PDBConstruct 1–523； UniProt 1–523

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	1irx
Deposition date deposition_date	2001-10-25
Structure title title	Crystal structure of class I lysyl-tRNA synthetase
Keywords keywords	;beta sandwitch, zinc-binding structure, Rossmann fold, alpha-helix cage, RIKEN Structural Genomics/Proteomics Initiative, RSGI, Structural Genomics, 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.

1irx__assembly_2__model_1

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

Download this curve (.dat)

1irx__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1irx__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	31.16 Å
Rg (electron density)	30.79 Å
Total Rg	31.21 Å
Atom count	4257
Residues	508
Excluded volume	75847 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1irx__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1irx__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 (3)

Entity 1 Entity 1 polymer

Description description	lysyl-tRNA synthetase
Molecular weight formula_weight	61656.4 kDa
EC 编号 ec_number	6.1.1.6
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	8754

MVHWADYIADKIIRERGEKEKYVVESGITPSGYVHVGNFRELFTAYIVGHALRDKGYEVRHIHMWDDYDRFRKVPRNVPQEWKDYLGMPISEVPDPWGCHESYAEHFMRKFEEEVEKLGIEVDLLYASELYKRGEYSEEIRLAFEKRDKIMEILNKYREIAKQPPLPENWWPAMVYCPEHRREAEIIEWDGGWKVKYKCPEGHEGWVDIRSGNVKLRWRVDWPMRWSHFGVDFEPAGKDHLVAGSSYDTGKEIIKEVYGKEAPLSLMYEFVGIKGQKGKMSGSKGNVILLSDLYEVLEPGLVRFIYARHRPNKEIKIDLGLGILNLYDEFEKVERIYFGVEGGKGDDEELRRTYELSMPKKPERLVAQAPFRFLAVLVQLPHLTEEDIINVLIKQGHIPRDLSKEDVERVKLRINLARNWVKKYAPEDVKFSILEKPPEVEVSEDVREAMNEVAEWLENHEEFSVEEFNNILFEVAKRRGISSREWFSTLYRLFIGKERGPRLASFLASLDRSFVIKRLRLEG

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 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	248

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6. Fold Classification (SCOP + CATH) 14 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d1irxa1
Class class	a — All alpha proteins
Fold Fold fold	a.97 — An anticodon-binding domain of class I aminoacyl-tRNA synthetases
Superfamily Superfamily superfamily	a.97.1 — An anticodon-binding domain of class I aminoacyl-tRNA synthetases
Family Family family	a.97.1.2 — C-terminal domain of class I lysyl-tRNA synthetase

Domain ID domain_id	d1irxa2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.26 — Adenine nucleotide alpha hydrolase-like
Superfamily Superfamily superfamily	c.26.1 — Nucleotidylyl transferase
Family Family family	c.26.1.1 — Class I aminoacyl-tRNA synthetases (RS), catalytic domain

Domain ID domain_id	d1irxb1
Class class	a — All alpha proteins
Fold Fold fold	a.97 — An anticodon-binding domain of class I aminoacyl-tRNA synthetases
Superfamily Superfamily superfamily	a.97.1 — An anticodon-binding domain of class I aminoacyl-tRNA synthetases
Family Family family	a.97.1.2 — C-terminal domain of class I lysyl-tRNA synthetase

Domain ID domain_id	d1irxb2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.26 — Adenine nucleotide alpha hydrolase-like
Superfamily Superfamily superfamily	c.26.1 — Nucleotidylyl transferase
Family Family family	c.26.1.1 — Class I aminoacyl-tRNA synthetases (RS), catalytic domain

CATH v4.4 (10 domains)

Domain ID domain_id	1irxA01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	620 — HUPs

Domain ID domain_id	1irxA02
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	30 — SH3 type barrels.
Homologous superfamily homologous superfamily	300 — class i lysyl-tRNA synthetase like

Domain ID domain_id	1irxA03
Class class	6 — Special
Architecture architecture	10 — Helix non-globular
Topology topology	20 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	10 — Lysine tRNA ligase, stem contact fold domain

Domain ID domain_id	1irxA04
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	770 —

Domain ID domain_id	1irxA05
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	350 —

Domain ID domain_id	1irxB01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	620 — HUPs

Domain ID domain_id	1irxB02
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	30 — SH3 type barrels.
Homologous superfamily homologous superfamily	300 — class i lysyl-tRNA synthetase like

Domain ID domain_id	1irxB03
Class class	6 — Special
Architecture architecture	10 — Helix non-globular
Topology topology	20 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	10 — Lysine tRNA ligase, stem contact fold domain

Domain ID domain_id	1irxB04
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	770 —

Domain ID domain_id	1irxB05
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	350 —

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Unit-cell length a length_a	58.945 Å
Unit-cell length b length_b	74.767 Å
Unit-cell length c length_c	156.945 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.26 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.600 Å
Low-resolution limit resolution_low	40.000 Å
R factor r_factor	—
R_work r_work	0.2250
R_free r_free	0.2920

Crystal structure of class I lysyl-tRNA synthetase

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

lysyl-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

1irx__assembly_2__model_1

1irx__assembly_2__model_1 | I(q)

1irx__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 (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) 14 domains

SCOP 2.08 (4 domains)

CATH v4.4 (10 domains)

7. Citations (1)

Crystal structure of class I lysyl-tRNA synthetase

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

lysyl-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

1irx__assembly_2__model_1

1irx__assembly_2__model_1 | I(q)

1irx__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 (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) 14 domains

SCOP 2.08 (4 domains)

CATH v4.4 (10 domains)

7. Citations (1)