SAXSdb — 6iy6

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

Aspartate--tRNA ligase, cytoplasmic

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 6	Aminoacyl tRNA synthase complex-interacting multifunctional protein 2 × 2 （Q13155） Bifunctional glutamate/proline--tRNA ligase × 2 （P07814） ZINC ION × 1 PHOSPHATE ION × 12 water × 3	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 6	Aminoacyl tRNA synthase complex-interacting multifunctional protein 2 × 2 （Q13155） Bifunctional glutamate/proline--tRNA ligase × 2 （P07814） ZINC ION × 1 PHOSPHATE ION × 5 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SYDC_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 22–502； UniProt 21–501 Author chain B； PDBConstruct 22–502； UniProt 21–501 Author chain G； PDBConstruct 22–502； UniProt 21–501 Author chain H； PDBConstruct 22–502； UniProt 21–501

Aminoacyl tRNA synthase complex-interacting multifunctional protein 2

Homo sapiens

UniProt Q13155

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 6	Aspartate--tRNA ligase, cytoplasmic × 2 （P14868） Bifunctional glutamate/proline--tRNA ligase × 2 （P07814） ZINC ION × 1 PHOSPHATE ION × 12 water × 3	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 6	Aspartate--tRNA ligase, cytoplasmic × 2 （P14868） Bifunctional glutamate/proline--tRNA ligase × 2 （P07814） ZINC ION × 1 PHOSPHATE ION × 5 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	AIMP2_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 2–207； UniProt 115–320 Author chain D； PDBConstruct 2–207； UniProt 115–320 Author chain I； PDBConstruct 2–207； UniProt 115–320 Author chain J； PDBConstruct 2–207； UniProt 115–320

Bifunctional glutamate/proline--tRNA ligase

Homo sapiens

UniProt P07814

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 6	Aspartate--tRNA ligase, cytoplasmic × 2 （P14868） Aminoacyl tRNA synthase complex-interacting multifunctional protein 2 × 2 （Q13155） ZINC ION × 1 PHOSPHATE ION × 12 water × 3	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 6	Aspartate--tRNA ligase, cytoplasmic × 2 （P14868） Aminoacyl tRNA synthase complex-interacting multifunctional protein 2 × 2 （Q13155） ZINC ION × 1 PHOSPHATE ION × 5 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SYEP_HUMAN
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain E； PDBConstruct 1–157； UniProt 1–157 Author chain F； PDBConstruct 1–157； UniProt 1–157 Author chain K； PDBConstruct 1–157； UniProt 1–157 Author chain L； PDBConstruct 1–157； UniProt 1–157

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	6iy6
Deposition date deposition_date	2018-12-13
Structure title title	Crystal structure of human cytosolic aspartyl-tRNA synthetase (DRS) in complex with glutathion-S transferase (GST) domains from Aminoacyl tRNA synthase complex-interacting multifunctional protein 2 (AIMP2) and glutamyl-prolyl-tRNA synthetase (EPRS)
Keywords keywords	Aminoacyl-tRNA transferase Glutathion-S transferase domain, TRANSLATION; TRANSLATION
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.

6iy6__assembly_1__model_1

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

Download this curve (.dat)

6iy6__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6iy6__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	43.79 Å
Rg (electron density)	43.84 Å
Total Rg	43.95 Å
Atom count	12304
Residues	1538
Excluded volume	219760 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6iy6__assembly_1__model_1`	hexameric （6）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`6iy6__assembly_2__model_1`	hexameric （6）	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 (6)

Entity 1 Entity 1 polymer

Description description	Aspartate--tRNA ligase, cytoplasmic
Molecular weight formula_weight	57310.1 kDa
EC 编号 ec_number	6.1.1.12
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,G,H
Atom count atom_count	24539

MGSSHHHHHHSSGLVPRGSHMAEDYAKERYGISSMIQSQEKPDRVLVRVRDLTIQKADEVVWVRARVHTSRAKGKQCFLVLRQQQFNVQALVAVGDHASKQMVKFAANINKESIVDVEGVVRKVNQKIGSCTQQDVELHVQKIYVISLAEPRLPLQLDDAVRPEAEGEEEGRATVNQDTRLDNRVIDLRTSTSQAVFRLQSGICHLFRETLINKGFVEIQTPKIISAASEGGANVFTVSYFKNNAYLAQSPQLYKQMCICADFEKVFSIGPVFRAEDSNTHRHLTEFVGLDIEMAFNYHYHEVMEEIADTMVQIFKGLQERFQTEIQTVNKQFPCEPFKFLEPTLRLEYCEALAMLREAGVEMGDEDDLSTPNEKLLGHLVKEKYDTDFYILDKYPLAVRPFYTMPDPRNPKQSNSYDMFMRGEEILSGAQRIHDPQLLTERALHHGIDLEKIKAYIDSFRFGAPPHAGGGIGLERVTMLFLGLHNVRQTSMFPRDPKRLTP

Source Source

Source organism organism	Homo sapiens
Common name common_name	Human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Aminoacyl tRNA synthase complex-interacting multifunctional protein 2
Molecular weight formula_weight	24165.0 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,D,I,J

MDYGALKDIVINANPASPPLSLLVLHRLLCEHFRVLSTVHTHSSVKSVPENLLKCFGEQNKKQPRQDYQLGFTLIWKNVPKTQMKFSIQTMCPIEGEGNIARFLFSLFGQKHNAVNATLIDSWVDIAIFQLKEGSSKEKAAVFRSMNSALGKSPWLAGNELTVADVVLWSVLQQIGGCSVTVPANVQRWMRSCENLAPFNTALKLLKLEHHHHHH

Source Source

Source organism organism	Homo sapiens
Common name common_name	Human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 polymer

Description description	Bifunctional glutamate/proline--tRNA ligase
Molecular weight formula_weight	18434.8 kDa
EC 编号 ec_number	6.1.1.17,6.1.1.15
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E,F,K,L

MATLSLTVNSGDPPLGALLAVEHVKDDVSISVEEGKENILHVSENVIFTDVNSILRYLARVATTAGLYGSNLMEHTEIDHWLEFSATKLSSCDSFTSTINELNHCLSLRTYLVGNSLSLADLCVWATLKGNAAWQEQLKQKKAPVHVKRWFGFLEAQLEHHHHHH

Source Source

Source organism organism	Homo sapiens
Common name common_name	Human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli

Entity 4 Entity 4 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 non-polymer

Description description	PHOSPHATE ION
Molecular weight formula_weight	95.0 kDa
Source method src_method	syn
Copy count entity_count	17

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	12

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6. Fold Classification (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

Domain ID domain_id	6iy6C00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1050 — Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2
Homologous superfamily homologous superfamily	130 —

Domain ID domain_id	6iy6D00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1050 — Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2
Homologous superfamily homologous superfamily	130 —

Domain ID domain_id	6iy6E00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1050 — Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2
Homologous superfamily homologous superfamily	130 —

Domain ID domain_id	6iy6F00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1050 — Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2
Homologous superfamily homologous superfamily	130 —

Domain ID domain_id	6iy6I00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1050 — Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2
Homologous superfamily homologous superfamily	130 —

Domain ID domain_id	6iy6J00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1050 — Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2
Homologous superfamily homologous superfamily	130 —

Domain ID domain_id	6iy6K00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1050 — Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2
Homologous superfamily homologous superfamily	130 —

Domain ID domain_id	6iy6L00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1050 — Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2
Homologous superfamily homologous superfamily	130 —

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Unit-cell length a length_a	108.068 Å
Unit-cell length b length_b	108.068 Å
Unit-cell length c length_c	815.642 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	24

Space group space_group	P 61
Space-group number int_tables_number	169
Crystal system crystal_system	—

Resolution resolution	3.600 Å
Low-resolution limit resolution_low	30.000 Å
R factor r_factor	0.2386
R_work r_work	0.2367
R_free r_free	0.2754

Crystal structure of human cytosolic aspartyl-tRNA synthetase (DRS) in complex with glutathion-S transferase (GST) domains from Aminoacyl tRNA synthase complex-interacting multifunctional protein 2 (AIMP2) and glutamyl-prolyl-tRNA synthetase (EPRS)

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

Aspartate--tRNA ligase, cytoplasmic

State in the Current Structure

Other States of the Same Protein in the Database

Aminoacyl tRNA synthase complex-interacting multifunctional protein 2

State in the Current Structure

Other States of the Same Protein in the Database

Bifunctional glutamate/proline--tRNA 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

6iy6__assembly_1__model_1

6iy6__assembly_1__model_1 | I(q)

6iy6__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 (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

7. Citations (1)

Crystal structure of human cytosolic aspartyl-tRNA synthetase (DRS) in complex with glutathion-S transferase (GST) domains from Aminoacyl tRNA synthase complex-interacting multifunctional protein 2 (AIMP2) and glutamyl-prolyl-tRNA synthetase (EPRS)

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

Aspartate--tRNA ligase, cytoplasmic

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Aminoacyl tRNA synthase complex-interacting multifunctional protein 2

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Bifunctional glutamate/proline--tRNA 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

6iy6__assembly_1__model_1

6iy6__assembly_1__model_1 | I(q)

6iy6__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 (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

7. Citations (1)