SAXSdb — 5xln

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

Eukaryotic translation initiation factor 4E type 2

Homo sapiens

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 45–234	Fragment：UNP residues 45-234	Threonine--tRNA ligase, cytoplasmic × 1 （P26639）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 9.5；295 K；20% PEG 8000, 0.1 M CHES (pH 9.5)	Resolution 1.90 Å R-free 0.196

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 5XLN	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2JGB Structure of human eIF4E homologous protein 4EHP with m7GTP Deposited 2007-02-12	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 45–234（190 aa） Fragment：RESIDUES 45-234	Not recorded	MGT 7N-METHYL-8-HYDROGUANOSINE-5'-TRIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.5；20% PEG-3000, 0.1M SODIUM CITRATE PH 5.5 WITH 1MM M7GTP IN THE DROP	Resolution 1.70 Å R-free 0.242
2JGC Structure of the human eIF4E homologous protein, 4EHP without ligand bound Deposited 2007-02-12	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 45–234（190 aa） Fragment：RESIDUES 45-234	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.5；20% PEG-3000, 0.1M SODIUM CITRATE PH 5.5	Resolution 2.40 Å R-free 0.249
5NVK Crystal structure of the human 4EHP-GIGYF1 complex Deposited 2017-05-04	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 52–234（183 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；20% PEG 3350 0.2 M KCl	Resolution 2.90 Å R-free 0.254
5NVK Crystal structure of the human 4EHP-GIGYF1 complex Deposited 2017-05-04	Different construct Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 52–234（183 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；20% PEG 3350 0.2 M KCl	Resolution 2.90 Å R-free 0.254
5NVK Crystal structure of the human 4EHP-GIGYF1 complex Deposited 2017-05-04	Different construct Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain E 52–234（183 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；20% PEG 3350 0.2 M KCl	Resolution 2.90 Å R-free 0.254
5NVK Crystal structure of the human 4EHP-GIGYF1 complex Deposited 2017-05-04	Different construct Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain G 52–234（183 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；20% PEG 3350 0.2 M KCl	Resolution 2.90 Å R-free 0.254
5NVL Crystal structure of the human 4EHP-GIGYF2 complex Deposited 2017-05-04	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 52–234（183 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；0.1 M sodium citrate pH 5.0 0.1 M magnesium chloride 12% PEG 4000	Resolution 2.30 Å R-free 0.242
5NVL Crystal structure of the human 4EHP-GIGYF2 complex Deposited 2017-05-04	Different construct Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 52–234（183 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；0.1 M sodium citrate pH 5.0 0.1 M magnesium chloride 12% PEG 4000	Resolution 2.30 Å R-free 0.242
5NVM Crystal structure of the human 4EHP-GIGYF2 complex lacking the auxiliary sequences Deposited 2017-05-04	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 52–234（183 aa）	Not recorded	PO4 PHOSPHATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；0.1 M sodium acetate pH 4.6 0.6 M diammonium phosphate	Resolution 2.00 Å R-free 0.233
5NVM Crystal structure of the human 4EHP-GIGYF2 complex lacking the auxiliary sequences Deposited 2017-05-04	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 52–234（183 aa）	Not recorded	PO4 PHOSPHATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；0.1 M sodium acetate pH 4.6 0.6 M diammonium phosphate	Resolution 2.00 Å R-free 0.233
5NVN Crystal structure of the human 4EHP-4E-BP1 complex Deposited 2017-05-04	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 52–234（183 aa）	Not recorded	FMT FORMIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.1 M sodium acetate pH 4.6 1.7 M sodium formate	Resolution 1.90 Å R-free 0.251
5NVN Crystal structure of the human 4EHP-4E-BP1 complex Deposited 2017-05-04	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 52–234（183 aa）	Not recorded	FMT FORMIC ACID × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.1 M sodium acetate pH 4.6 1.7 M sodium formate	Resolution 1.90 Å R-free 0.251

6 other PDB entries and 12 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	IF4E2_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–190； UniProt 45–234

Threonine--tRNA ligase, cytoplasmic

Homo sapiens

UniProt P26639

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain B； UniProt 30–74	Fragment：UNP residues 30-74	Eukaryotic translation initiation factor 4E type 2 × 1 （O60573）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 9.5；295 K；20% PEG 8000, 0.1 M CHES (pH 9.5)	Resolution 1.90 Å R-free 0.196

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 5XLN	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1WWT Solution structure of the TGS domain from human threonyl-tRNA synthetase Deposited 2005-01-18	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 67–141（75 aa） Fragment：TGS domain	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7；296 K；Ionic strength (raw mmCIF value) 120mM；Pressure ambient NMR sample composition 1.20mM TGS domain U-15N,13C; 20mM d-tris-HCl(pH 7.0); 100mM NaCl; 1mM d-DTT; 0.02% NaN3; 10% D2O \| 90% H2O/10% D2O	Resolution not provided
4HWT Crystal structure of human Threonyl-tRNA synthetase bound to a novel inhibitor Deposited 2012-11-08	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 321–723（403 aa） Fragment：UNP residues 321-723 Chain B 321–723（403 aa） Fragment：UNP residues 321-723	Not recorded	ZN ZINC ION × 2 1B2 N-{[3-(2H-indazol-5-yl)phenyl]sulfonyl}-L-threoninamide × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.9；298 K；PEG 3350, sodium citrate, pH 7.9, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.30 Å R-free 0.257
4P3N Structural Basis for Full-Spectrum Inhibition of Threonyl-tRNA Synthetase by Borrelidin 1 Deposited 2014-03-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 322–723（402 aa） Fragment：UNP residues 322-723 Chain B 322–723（402 aa） Fragment：UNP residues 322-723	Not recorded	2CR (1R,2R)-2-[(2S,4E,6E,8R,9S,11R,13S,15S,16S)-7-cyano-8,16-dihydroxy-9,11,13,15-tetramethyl-18-oxooxacyclooctadeca-4,6-dien-2-yl]cyclopentanecarboxylic acid × 2 ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；Calcium Acetate, PEG4000, Sodium Acetate	Resolution 2.60 Å R-free 0.255
4P3N Structural Basis for Full-Spectrum Inhibition of Threonyl-tRNA Synthetase by Borrelidin 1 Deposited 2014-03-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 322–723（402 aa） Fragment：UNP residues 322-723 Chain D 322–723（402 aa） Fragment：UNP residues 322-723	Not recorded	2CR (1R,2R)-2-[(2S,4E,6E,8R,9S,11R,13S,15S,16S)-7-cyano-8,16-dihydroxy-9,11,13,15-tetramethyl-18-oxooxacyclooctadeca-4,6-dien-2-yl]cyclopentanecarboxylic acid × 2 ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；Calcium Acetate, PEG4000, Sodium Acetate	Resolution 2.60 Å R-free 0.255
4TTV Crystal structure of human ThrRS complexing with a bioengineered macrolide BC194 Deposited 2014-06-23	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 322–723（402 aa） Fragment：UNP residues 322-723 Chain B 322–723（402 aa） Fragment：UNP residues 322-723	Not recorded	BC9 (1R,2R)-2-[(2S,6E,8R,9S,11R,13S,15S,16S)-7-cyano-8,16-dihydroxy-9,11,13,15-tetramethyl-18-oxooxacyclooctadec-6-en-2-yl]cyclobutanecarboxylic acid × 2 ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；291 K；Tris, PEG8000	Resolution 2.80 Å R-free 0.288
4TTV Crystal structure of human ThrRS complexing with a bioengineered macrolide BC194 Deposited 2014-06-23	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 322–723（402 aa） Fragment：UNP residues 322-723 Chain D 322–723（402 aa） Fragment：UNP residues 322-723	Not recorded	BC9 (1R,2R)-2-[(2S,6E,8R,9S,11R,13S,15S,16S)-7-cyano-8,16-dihydroxy-9,11,13,15-tetramethyl-18-oxooxacyclooctadec-6-en-2-yl]cyclobutanecarboxylic acid × 2 ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；291 K；Tris, PEG8000	Resolution 2.80 Å R-free 0.288

4 other PDB entries and 6 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	SYTC_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–45； UniProt 30–74

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	5xln
Deposition date deposition_date	2017-05-11
Structure title title	Crystal structure of the TRS_UNE-T and 4EHP complex
Keywords keywords	TRS, 4EHP, Complex, RNA BINDING PROTEIN-LIGASE complex; RNA BINDING PROTEIN/LIGASE
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	17.74 Å
Radius of gyration Rg (electron density) rg_electron	16.44 Å
Forward intensity I(0) i0	9121530.00
Molecular weight molecular_weight	22338.0 kDa
Excluded volume excluded_volume	28003 Å³
Envelope volume envelope_volume	32912 Å³
Hydration-shell volume shell_volume	16566 Å³
Envelope diameter envelope_diameter	59.3 Å
Shell Rg shell_rg	22.73 Å
Envelope Rg envelope_rg	17.07 Å
Shape Rg shape_rg	16.42 Å
Total Rg total_rg	17.56 Å
Total atoms total_atoms	1577
Residues n_residues	191
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	65.2 Å
Rg (real space) rg_real	17.62 Å
Rg uncertainty (real space) rg_real_error	0.54 Å
I(0) (real space) i0_real	9.1220e+06
I(0) uncertainty (real space) i0_real_error	1.1790e+05
Rg (reciprocal space) rg_reciprocal	17.64 Å
I(0) (reciprocal space) i0_reciprocal	9122000.0000
Solution quality estimate total_estimate	0.7348
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	23.5 Å
Skewness Skewness skewness	0.168
Kurtosis Kurtosis kurtosis	-0.263
Angular range angular_range	— – 0.4500 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	2539000.0000
Real-space data points n_real_points	76
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.537; Stabil: 0.990; Sysdev: 1.000; Positv: 1.000; Valcen: 0.967; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Eukaryotic translation initiation factor 4E type 2
Molecular weight formula_weight	21963.1 kDa
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	1754

KAVVPGPAEHPLQYNYTFWYSRRTPGRPTSSQSYEQNIKQIGTFASVEQFWRFYSHMVRPGDLTGHSDFHLFKEGIKPMWEDDANKNGGKWIIRLRKGLASRCWENLILAMLGEQFMVGEEICGAVVSVRFQEDIISIWNKTASDQATTARIRDTLRRVLNLPPNTIMEYKTHTDSIKMPGRLGPQRLLF

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	Human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Threonine--tRNA ligase, cytoplasmic
Molecular weight formula_weight	5087.7 kDa
EC 编号 ec_number	6.1.1.3
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

GGKKKNKEGSGDGGRAELNPWPEYIYTRLEMYNILKAEHDSILAE

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	Human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	177

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d5xlna_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.86 — eIF4e-like
Superfamily Superfamily superfamily	d.86.1 — eIF4e-like
Family Family family	d.86.1.0 — automated matches

CATH v4.4 (1 domains)

Domain ID domain_id	5xlnA01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	760 — RNA Cap, Translation Initiation Factor Eif4e
Homologous superfamily homologous superfamily	10 — RNA Cap, Translation Initiation Factor Eif4e

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8. Citations (1)

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Unit-cell length a length_a	49.369 Å
Unit-cell length b length_b	60.569 Å
Unit-cell length c length_c	85.237 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	1.900 Å
Low-resolution limit resolution_low	25.815 Å
R factor r_factor	0.1628
R_work r_work	0.1610
R_free r_free	0.1964

fit	/app/data/saxs_computation/xl/5xln/5xln.fit
pddf	/app/data/pr_computation/xl/5xln/5xln.pr.out
profile	/app/data/saxs_computation/xl/5xln/5xln.dat

Crystal structure of the TRS_UNE-T and 4EHP complex

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

Eukaryotic translation initiation factor 4E type 2

State in the Current Structure

Other States of the Same Protein in the Database

Threonine--tRNA ligase, cytoplasmic

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 water

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)