SAXSdb — 4bvx

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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 2	EUKARYOTIC TRANSLATION ELONGATION FACTOR 1 EPSILON-1 × 1 （O43324） 5-amino-2,4,6-triiodobenzene-1,3-dicarboxylic acid × 3 water × 2	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 1–207； UniProt 1–207

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 2	METHIONINE--TRNA LIGASE, CYTOPLASMIC × 1 （P56192） 5-amino-2,4,6-triiodobenzene-1,3-dicarboxylic acid × 3 water × 2	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 3–171； UniProt 1–169

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	4bvx
Deposition date deposition_date	2013-06-29
Structure title title	Crystal structure of the AIMP3-MRS N-terminal domain complex with I3C
Keywords keywords	LIGASE, MRS; 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.

4bvx__assembly_1__model_1

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

Download this curve (.dat)

4bvx__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4bvx__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	22.49 Å
Rg (electron density)	21.02 Å
Total Rg	22.19 Å
Atom count	2997
Residues	373
Excluded volume	53598 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4bvx__assembly_1__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 (4)

Entity 1 Entity 1 polymer

Description description	METHIONINE--TRNA LIGASE, CYTOPLASMIC
Molecular weight formula_weight	24060.4 kDa
EC 编号 ec_number	6.1.1.10
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	3247

MRLFVSDGVPGCLPVLAAAGRARGRAEVLISTVGPQDCVVPFLTRPKVPVLQLDSGNYLFSTSAICRYFFLLSGWEQDDLTNQWLEWEATELQPALSAALYYLVVQGKKGEDVLGSVRRALTHIDHSLSRQNCPFLAGETESLADIVLWGALYPLLQDPAYLPEELSALHSWFQTLSTQEPCQRAAQTVLKQQGVLALRPYLQKQPQLEHHHHHH

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	19479.3 kDa
Mutation mutation	YES
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

GHMAAAAELSLLEKSLGLSKGNKYSAQGERQIPVLQTNDGPSLMGLTTIAAHLVKQANKEYLLGSTAEEKAMVQQWLEYRVTQVDGHSSKNDIHTLLMDLNSYLEDKVYLTGYNFTLADILLYYGLHRFIVDLTVQEKEKYLNVSRWFCHIQHYPGIRQHLSSVVFIKNRL

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 non-polymer

Description description	5-amino-2,4,6-triiodobenzene-1,3-dicarboxylic acid
Molecular weight formula_weight	558.8 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	178

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6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	4bvxA01
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	4bvxA02
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	4bvxB01
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	4bvxB02
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 —

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Unit-cell length a length_a	43.284 Å
Unit-cell length b length_b	71.584 Å
Unit-cell length c length_c	116.381 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 2 21 21
Space-group number int_tables_number	18
Crystal system crystal_system	—

Resolution resolution	1.600 Å
Low-resolution limit resolution_low	30.490 Å
R factor r_factor	0.2183
R_work r_work	0.2168
R_free r_free	0.2466

Crystal structure of the AIMP3-MRS N-terminal domain complex with I3C

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

EUKARYOTIC TRANSLATION ELONGATION FACTOR 1 EPSILON-1

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

4bvx__assembly_1__model_1

4bvx__assembly_1__model_1 | I(q)

4bvx__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 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)

Crystal structure of the AIMP3-MRS N-terminal domain complex with I3C

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

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

4bvx__assembly_1__model_1

4bvx__assembly_1__model_1 | I(q)

4bvx__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 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)