SAXSdb — 4l87

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

Serine--tRNA ligase, cytoplasmic

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 homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 2–477	Fragment：UNP residues 2-477	SSA 5'-O-(N-(L-SERYL)-SULFAMOYL)ADENOSINE × 2 PO4 PHOSPHATE ION × 2 MG MAGNESIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7；298 K；20% PEG3350, 0.2 M ammonium fluoride or ammonium formate, 0.1 M HEPES, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 2.90 Å R-free 0.268

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 4L87	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
3VBB Crystal Structure of Seryl-tRNA Synthetase from Human at 2.9 angstroms Deposited 2012-01-02	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–514（514 aa） Chain B 1–514（514 aa）	Not recorded	MG MAGNESIUM ION × 2 PO4 PHOSPHATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；298 K；20% PEG 3350, 0.2 M tri-sodium citrate pH 7.0, 5mM ATP, 10mM MgCl2, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 2.89 Å R-free 0.250
3VBB Crystal Structure of Seryl-tRNA Synthetase from Human at 2.9 angstroms Deposited 2012-01-02	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 1–514（514 aa） Chain D 1–514（514 aa）	Not recorded	PO4 PHOSPHATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；298 K；20% PEG 3350, 0.2 M tri-sodium citrate pH 7.0, 5mM ATP, 10mM MgCl2, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 2.89 Å R-free 0.250
3VBB Crystal Structure of Seryl-tRNA Synthetase from Human at 2.9 angstroms Deposited 2012-01-02	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain E 1–514（514 aa） Chain F 1–514（514 aa）	Not recorded	PO4 PHOSPHATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；298 K；20% PEG 3350, 0.2 M tri-sodium citrate pH 7.0, 5mM ATP, 10mM MgCl2, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 2.89 Å R-free 0.250
4RQE human Seryl-tRNA synthetase dimer complexed with two molecules of tRNAsec Deposited 2014-11-03	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Homooligomer；Protein × 2 PDB declaration: tetrameric	Chain A 1–514（514 aa） Chain C 1–514（514 aa）	Mutation：E156T, R157S Mutation：E156T, R157S	SER SERINE × 2 ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7；298 K；18%(m/v) PEG3350, 0.1M NaCl, 0.1M Tris-HCl (pH8.0), 0.1M Sodium malonate pH7.0. , VAPOR DIFFUSION, temperature 298K	Resolution 4.00 Å R-free 0.322
4RQF human Seryl-tRNA synthetase dimer complexed with one molecule of tRNAsec Deposited 2014-11-03	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Homooligomer；Protein × 2 PDB declaration: trimeric	Chain A 1–514（514 aa） Chain B 1–514（514 aa）	Mutation：E447K Mutation：E447K	ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 2 SER SERINE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7；298 K；18%(m/v) PEG3350, 0.1M NaCl, 0.1M Tris-HCl (pH8.0), 0.1M Sodium malonate pH7.0., VAPOR DIFFUSION, temperature 298K	Resolution 3.50 Å R-free 0.314
8P7B CryoEM structure of METTL6 tRNA SerRS complex in a 1:2:2 stoichiometry Deposited 2023-05-30	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 3 PDB declaration: pentameric	Chain B 1–514（514 aa） Chain D 1–514（514 aa）	Not recorded	SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 MG MAGNESIUM ION × 6	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.42 Å
8P7C CryoEM structure of METTL6 tRNA SerRS complex in a 2:2:2 stoichiometry Deposited 2023-05-30	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 4 PDB declaration: hexameric	Chain B 1–514（514 aa） Chain D 1–514（514 aa）	Not recorded	SAH S-ADENOSYL-L-HOMOCYSTEINE × 2 MG MAGNESIUM ION × 6	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.70 Å
8P7D CryoEM structure of METTL6 tRNA SerRS complex in a 1:1:2 stoichiometry Deposited 2023-05-30	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 3 PDB declaration: tetrameric	Chain B 1–514（514 aa） Chain D 1–514（514 aa）	Not recorded	SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 MG MAGNESIUM ION × 3	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.20 Å
9DPD Cryo-EM structure of SerRS dimer in complex with one SIRT2 Deposited 2024-09-21	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 1–514（514 aa） Chain D 1–514（514 aa）	Not recorded	AR6 [(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL[HYDROXY-[[(2R,3S,4R,5S)-3,4,5-TRIHYDROXYOXOLAN-2-YL]METHOXY]PHOSPHORYL] HYDROGEN PHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.87 Å
9DPI Cryo-EM structure of SerRS dimer in complex with two SIRT2 Deposited 2024-09-21	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain D 1–514（514 aa） Chain F 1–514（514 aa）	Not recorded	AR6 [(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL[HYDROXY-[[(2R,3S,4R,5S)-3,4,5-TRIHYDROXYOXOLAN-2-YL]METHOXY]PHOSPHORYL] HYDROGEN PHOSPHATE × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；in 25mM HEPES-Na pH7.5, 150mM NaCl cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.90 Å

8 other PDB entries and 10 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	SYSC_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–476； UniProt 2–477

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	4l87
Deposition date deposition_date	2013-06-16
Structure title title	Crystal structure of the human seryl-tRNA synthetase in complex with Ser-SA at 2.9 Angstrom resolution
Keywords keywords	long alpha-helices, seven-stranded anti-parallel beta-sheet, aminoacylation, tRNAser, LIGASE; 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	29.17 Å
Radius of gyration Rg (electron density) rg_electron	29.64 Å
Forward intensity I(0) i0	49804000.00
Molecular weight molecular_weight	54992.0 kDa
Excluded volume excluded_volume	68795 Å³
Envelope volume envelope_volume	89539 Å³
Hydration-shell volume shell_volume	27908 Å³
Envelope diameter envelope_diameter	115.4 Å
Shell Rg shell_rg	32.98 Å
Envelope Rg envelope_rg	30.75 Å
Shape Rg shape_rg	29.60 Å
Total Rg total_rg	30.12 Å
Total atoms total_atoms	3863
Residues n_residues	476
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	110.1 Å
Rg (real space) rg_real	29.63 Å
Rg uncertainty (real space) rg_real_error	1.06 Å
I(0) (real space) i0_real	4.9800e+07
I(0) uncertainty (real space) i0_real_error	8.3950e+05
Rg (reciprocal space) rg_reciprocal	29.43 Å
I(0) (reciprocal space) i0_reciprocal	49800000.0000
Solution quality estimate total_estimate	0.7524
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	28.5 Å
Skewness Skewness skewness	0.814
Kurtosis Kurtosis kurtosis	0.344
Angular range angular_range	— – 0.2700 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	9875000.0000
Real-space data points n_real_points	55
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.446; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.555; Smooth: 0.884

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Serine--tRNA ligase, cytoplasmic
Molecular weight formula_weight	54517.2 kDa
EC 编号 ec_number	6.1.1.11
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	3863

VLDLDLFRVDKGGDPALIRETQEKRFKDPGLVDQLVKADSEWRRCRFRADNLNKLKNLCSKTIGEKMKKKEPVGDDESVPENVLSFDDLTADALANLKVSQIKKVRLLIDEAILKCDAERIKLEAERFENLREIGNLLHPSVPISNDEDVDNKVERIWGDCTVRKKYSHVDLVVMVDGFEGEKGAVVAGSRGYFLKGVLVFLEQALIQYALRTLGSRGYIPIYTPFFMRKEVMQEVAQLSQFDEELYKVIGKGSEKSDDNSYDEKYLIATSEQPIAALHRDEWLRPEDLPIKYAGLSTCFRQEVGSHGRDTRGIFRVHQFEKIEQFVYSSPHDNKSWEMFEEMITTAEEFYQSLGIPYHIVNIVSGSLNHAASKKLDLEAWFPGSGAFRELVSCSNCTDYQARRLRIRYGQTKKMMDKVEFVHMLNATMCATTRTICAILENYQTEKGITVPEKLKEFMPPGLQELIPFVKPAPIE

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 non-polymer

Description description	5'-O-(N-(L-SERYL)-SULFAMOYL)ADENOSINE
Molecular weight formula_weight	433.4 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	PHOSPHATE ION
Molecular weight formula_weight	95.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	2

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7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	4l87A01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	287 — Helix Hairpins
Homologous superfamily homologous superfamily	40 — Serine-tRNA synthetase, tRNA binding domain

Domain ID domain_id	4l87A02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	930 — BirA Bifunctional Protein; domain 2
Homologous superfamily homologous superfamily	10 — Bira Bifunctional Protein; Domain 2

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8. Citations (1)

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Unit-cell length a length_a	167.074 Å
Unit-cell length b length_b	167.074 Å
Unit-cell length c length_c	65.156 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	6

Space group space_group	P 3 2 1
Space-group number int_tables_number	150
Crystal system crystal_system	—

Resolution resolution	2.897 Å
Low-resolution limit resolution_low	144.690 Å
R factor r_factor	0.2556
R_work r_work	0.2549
R_free r_free	0.2676

fit	/app/data/saxs_computation/l8/4l87/4l87.fit
pddf	/app/data/pr_computation/l8/4l87/4l87.pr.out
profile	/app/data/saxs_computation/l8/4l87/4l87.dat

Crystal structure of the human seryl-tRNA synthetase in complex with Ser-SA at 2.9 Angstrom resolution

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

Serine--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