SAXSdb — 5y6l

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

Methionine--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 5	Eukaryotic translation elongation factor 1 epsilon-1 × 1 （O43324） Bifunctional glutamate/proline--tRNA ligase × 1 （P07814） Aminoacyl tRNA synthase complex-interacting multifunctional protein 2 × 1 （Q13155） Aspartate--tRNA ligase, cytoplasmic × 1 （P14868） PHOSPHATE ION × 2 water × 5	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SYMC_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–224； UniProt 1–224

Eukaryotic translation elongation factor 1 epsilon-1

Homo sapiens

UniProt O43324

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 5	Methionine--tRNA ligase, cytoplasmic × 1 （P56192） Bifunctional glutamate/proline--tRNA ligase × 1 （P07814） Aminoacyl tRNA synthase complex-interacting multifunctional protein 2 × 1 （Q13155） Aspartate--tRNA ligase, cytoplasmic × 1 （P14868） PHOSPHATE ION × 2 water × 5	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	MCA3_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 13–186； UniProt 1–174

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 5	Methionine--tRNA ligase, cytoplasmic × 1 （P56192） Eukaryotic translation elongation factor 1 epsilon-1 × 1 （O43324） Aminoacyl tRNA synthase complex-interacting multifunctional protein 2 × 1 （Q13155） Aspartate--tRNA ligase, cytoplasmic × 1 （P14868） PHOSPHATE ION × 2 water × 5	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 C； PDBConstruct 1–175； UniProt 1–175

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 5	Methionine--tRNA ligase, cytoplasmic × 1 （P56192） Eukaryotic translation elongation factor 1 epsilon-1 × 1 （O43324） Bifunctional glutamate/proline--tRNA ligase × 1 （P07814） Aspartate--tRNA ligase, cytoplasmic × 1 （P14868） PHOSPHATE ION × 2 water × 5	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	4
Chains and sequence ranges	Author chain D； PDBConstruct 2–232； UniProt 90–320

Aspartate--tRNA ligase, cytoplasmic

Homo sapiens

UniProt P14868

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 5	Methionine--tRNA ligase, cytoplasmic × 1 （P56192） Eukaryotic translation elongation factor 1 epsilon-1 × 1 （O43324） Bifunctional glutamate/proline--tRNA ligase × 1 （P07814） Aminoacyl tRNA synthase complex-interacting multifunctional protein 2 × 1 （Q13155） PHOSPHATE ION × 2 water × 5	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	5
Chains and sequence ranges	Author chain E； PDBConstruct 21–521； UniProt 1–501

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	5y6l
Deposition date deposition_date	2017-08-12
Structure title title	A subcomplex crystal structure of human cytosolic aspartyl-tRNA synthetase and heterotetrameric glutathione transferase-homology domains in multi-tRNA synthetase complex
Keywords keywords	AMINO-ACYL TRNA SYNTHETASE COMPLEX, MULTI-SYNTHETASE COMPLEX, LIGATION AMINO ACID TO TRNA, 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.

5y6l__assembly_1__model_1

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

Download this curve (.dat)

5y6l__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5y6l__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	33.14 Å
Rg (electron density)	32.69 Å
Total Rg	33.22 Å
Atom count	6380
Residues	825
Excluded volume	113940 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5y6l__assembly_1__model_1`	pentameric （5）	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 (7)

Entity 1 Entity 1 polymer

Description description	Methionine--tRNA ligase, cytoplasmic
Molecular weight formula_weight	25956.4 kDa
EC 编号 ec_number	6.1.1.10
Mutation mutation	S171R
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	6458

MRLFVSDGVPGCLPVLAAAGRARGRAEVLISTVGPEDCVVPFLTRPKVPVLQLDSGNYLFSTSAICRYFFLLSGWEQDDLTNQWLEWEATELQPALSAALYYLVVQGKKGEDVLGSVRRALTHIDHSLSRQNCPFLAGETESLADIVLWGALYPLLQDPAYLPEELSALHRWFQTLSTQEPCQRAAETVLKQQGVLALRPYLQKQPQPSPAEGRAVTNEPEEEELEHHHHHH

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	Eukaryotic translation elongation factor 1 epsilon-1
Molecular weight formula_weight	21226.0 kDa
Mutation mutation	C147S
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

MRGSHHHHHHGSMAAAAELSLLEKSLGLSKGNKYSAQGERQIPVLQTNNGPSLTGLTTIAAHLVKQANKEYLLGSTAEEKAIVQQWLEYRVTQVDGHSSKNDIHTLLKDLNSYLEDKVYLTGYNFTLADILLYYGLHRFIVDLTVQEKEKYLNVSRWFSHIQHYPGIRQHLSSVVFIKNRLYTNSH

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 BL21(DE3)

Entity 3 Entity 3 polymer

Description description	Bifunctional glutamate/proline--tRNA ligase
Molecular weight formula_weight	19310.7 kDa
EC 编号 ec_number	6.1.1.17
Mutation mutation	C92S, C105S, C123S
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

MATLSLTVNSGDPPLGALLAVEHVKDDVSISVEEGKENILHVSENVIFTDVNSILRYLARVATTAGLYGSNLMEHTEIDHWLEFSATKLSSSDSFTSTINELNHSLSLRTYLVGNSLSLADLSVWATLKGNAAWQEQLKQKKAPVHVKRWFGFLEAQQAFQSVGTKWDVSTTKAR

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 polymer

Description description	Aminoacyl tRNA synthase complex-interacting multifunctional protein 2
Molecular weight formula_weight	26790.9 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D

MTNIIQADEPTTLTTNALDLNSVLGKDYGALKDIVINANPASPPLSLLVLHRLLCEHFRVLSTVHTHSSVKSVPENLLKCFGEQNKKQPRQDYQLGFTLIWKNVPKTQMKFSIQTMCPIEGEGNIARFLFSLFGQKHNAVNATLIDSWVDIAIFQLKEGSSKEKAAVFRSMNSALGKSPWLAGNELTVADVVLWSVLQQIGGCSVTVPANVQRWMRSCENLAPFNTALKLLKLEHHHHHH

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 5 Entity 5 polymer

Description description	Aspartate--tRNA ligase, cytoplasmic
Molecular weight formula_weight	59384.4 kDa
EC 编号 ec_number	6.1.1.12
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E

MGSSHHHHHHSSGLVPRGSHMPSASASRKSQEKPREIMDAAEDYAKERYGISSMIQSQEKPDRVLVRVRDLTIQKADEVVWVRARVHTSRAKGKQCFLVLRQQQFNVQALVAVGDHASKQMVKFAANINKESIVDVEGVVRKVNQKIGSCTQQDVELHVQKIYVISLAEPRLPLQLDDAVRPEAEGEEEGRATVNQDTRLDNRVIDLRTSTSQAVFRLQSGICHLFRETLINKGFVEIQTPKIISAASEGGANVFTVSYFKNNAYLAQSPQLYKQMCICADFEKVFSIGPVFRAEDSNTHRHLTEFVGLDIEMAFNYHYHEVMEEIADTMVQIFKGLQERFQTEIQTVNKQFPCEPFKFLEPTLRLEYCEALAMLREAGVEMGDEDDLSTPNEKLLGHLVKEKYDTDFYILDKYPLAVRPFYTMPDPRNPKQSNSYDMFMRGEEILSGAQRIHDPQLLTERALHHGIDLEKIKAYIDSFRFGAPPHAGGGIGLERVTMLFLGLHNVRQTSMFPRDPKRLTP

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 6 Entity 6 non-polymer

Description description	PHOSPHATE ION
Molecular weight formula_weight	95.0 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 7 Entity 7 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	78

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6. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

Domain ID domain_id	5y6lA01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	30 — Glutaredoxin
Homologous superfamily homologous superfamily	10 — Glutaredoxin

Domain ID domain_id	5y6lA02
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	10 —

Domain ID domain_id	5y6lB01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	30 — Glutaredoxin
Homologous superfamily homologous superfamily	90 —

Domain ID domain_id	5y6lB02
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	10 —

Domain ID domain_id	5y6lC00
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	5y6lD00
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	84.535 Å
Unit-cell length b length_b	98.413 Å
Unit-cell length c length_c	125.919 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	4

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.900 Å
Low-resolution limit resolution_low	29.873 Å
R factor r_factor	0.1828
R_work r_work	0.1765
R_free r_free	0.2518

A subcomplex crystal structure of human cytosolic aspartyl-tRNA synthetase and heterotetrameric glutathione transferase-homology domains in multi-tRNA synthetase complex

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

Methionine--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

Eukaryotic translation elongation factor 1 epsilon-1

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

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

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

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

5y6l__assembly_1__model_1

5y6l__assembly_1__model_1 | I(q)

5y6l__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 (7)

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 polymer

Polymer Polymer

Source Source

Entity 5 Entity 5 polymer

Polymer Polymer

Source Source

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

6. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

7. Citations (1)