SAXSdb — 9otp

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

Glutamine synthetase

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 × 10 PDB declaration: decameric（10） Consistent with protein copy count	Chain A； UniProt 1–373 Chain B； UniProt 1–373 Chain C； UniProt 1–373 Chain D； UniProt 1–373 Chain E； UniProt 1–373 Chain F； UniProt 1–373 Chain G； UniProt 1–373 Chain H； UniProt 1–373 Chain I； UniProt 1–373 Chain J； UniProt 1–373	Mutation：R298A	ADP ADENOSINE-5'-DIPHOSPHATE × 10 MG MAGNESIUM ION × 20	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.6 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 1.95 Å

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 9OTP	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2OJW Crystal structure of human glutamine synthetase in complex with ADP and phosphate Deposited 2007-01-15	Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 10 PDB declaration: decameric	Chain A 4–364（361 aa） Fragment：Residues 4-364 Chain B 4–364（361 aa） Fragment：Residues 4-364 Chain C 4–364（361 aa） Fragment：Residues 4-364 Chain D 4–364（361 aa） Fragment：Residues 4-364 Chain E 4–364（361 aa） Fragment：Residues 4-364	Not recorded	MN MANGANESE (II) ION × 40 PO4 PHOSPHATE ION × 10 CL CHLORIDE ION × 10 ADP ADENOSINE-5'-DIPHOSPHATE × 10 GOL GLYCEROL × 12	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；277 K；10% Isopropanol, 200 mM NaCl, 100 mM HEPES, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K, pH 7.50	Resolution 2.05 Å R-free 0.212
2QC8 Crystal structure of human glutamine synthetase in complex with ADP and methionine sulfoximine phosphate Deposited 2007-06-19	Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 10 PDB declaration: decameric	Chain A 5–365（361 aa） Chain B 5–365（361 aa） Chain C 5–365（361 aa） Chain D 5–365（361 aa） Chain E 5–365（361 aa） Chain F 5–365（361 aa） Chain G 5–365（361 aa） Chain H 5–365（361 aa） Chain I 5–365（361 aa） Chain J 5–365（361 aa）	Not recorded	MN MANGANESE (II) ION × 30 CL CHLORIDE ION × 10 ADP ADENOSINE-5'-DIPHOSPHATE × 10 P3S L-METHIONINE-S-SULFOXIMINE PHOSPHATE × 10	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；298 K；1.1M Sodium malonate, 0.5% Jeffamine ED-2001, 0.1M HEPES, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K, pH 7.00	Resolution 2.60 Å R-free 0.217
7EVT Crystal structure of the N-terminal degron-truncated human glutamine synthetase Deposited 2021-05-22	Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 10 PDB declaration: decameric	Chain A 23–373（351 aa） Chain B 23–373（351 aa） Chain C 23–373（351 aa） Chain D 23–373（351 aa） Chain E 23–373（351 aa） Chain F 23–373（351 aa） Chain G 23–373（351 aa） Chain H 23–373（351 aa） Chain I 23–373（351 aa） Chain J 23–373（351 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.1；293.15 K；0.07 M sodium citrate (pH 5.1), 10% glycerol and 5.6% PEG4000	Resolution 2.95 Å R-free 0.250
8DNU Human Brain Glutamine Synthetase Deposited 2022-07-11	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 10 PDB declaration: decameric	Chain A 1–373（373 aa） Chain B 1–373（373 aa） Chain C 1–373（373 aa） Chain D 1–373（373 aa） Chain E 1–373（373 aa） Chain F 1–373（373 aa） Chain G 1–373（373 aa） Chain H 1–373（373 aa） Chain I 1–373（373 aa） Chain J 1–373（373 aa）	Not recorded	MN MANGANESE (II) ION × 10	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.73 Å
9NLR Crystal structure of human glutamine synthetase in complex with ADP and phosphate Deposited 2025-03-03	Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 10 PDB declaration: decameric	Chain A 1–373（373 aa） Chain B 1–373（373 aa） Chain C 1–373（373 aa） Chain D 1–373（373 aa） Chain E 1–373（373 aa） Chain F 1–373（373 aa） Chain G 1–373（373 aa） Chain H 1–373（373 aa） Chain I 1–373（373 aa） Chain J 1–373（373 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 10 MN MANGANESE (II) ION × 30 PO4 PHOSPHATE ION × 10 NA SODIUM ION × 11	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.5；291 K；30% (v/v) 2-methyl-2,4-pentanediol, 100 mM Tris pH 8.5, 500 mM NaCl, 8% (w/v) PEG 8000	Resolution 2.30 Å R-free 0.215
9NLR Crystal structure of human glutamine synthetase in complex with ADP and phosphate Deposited 2025-03-03	Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 10 PDB declaration: decameric	Chain K 1–373（373 aa） Chain L 1–373（373 aa） Chain M 1–373（373 aa） Chain N 1–373（373 aa） Chain O 1–373（373 aa） Chain P 1–373（373 aa） Chain Q 1–373（373 aa） Chain R 1–373（373 aa） Chain S 1–373（373 aa） Chain T 1–373（373 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 10 MN MANGANESE (II) ION × 30 PO4 PHOSPHATE ION × 10 NA SODIUM ION × 10	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.5；291 K；30% (v/v) 2-methyl-2,4-pentanediol, 100 mM Tris pH 8.5, 500 mM NaCl, 8% (w/v) PEG 8000	Resolution 2.30 Å R-free 0.215
9NM5 Crystal structure of human glutamine synthetase in complex with ADP and phosphinothricin phosphate Deposited 2025-03-04	Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 10 PDB declaration: decameric	Chain A 1–373（373 aa） Chain B 1–373（373 aa） Chain C 1–373（373 aa） Chain D 1–373（373 aa） Chain E 1–373（373 aa） Chain F 1–373（373 aa） Chain G 1–373（373 aa） Chain H 1–373（373 aa） Chain I 1–373（373 aa） Chain J 1–373（373 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	ADP ADENOSINE-5'-DIPHOSPHATE × 10 MN MANGANESE (II) ION × 30 P3P (2S)-2-AMINO-4-[METHYL(PHOSPHONOOXY)PHOSPHORYL]BUTANOIC ACID × 10 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 21 CL CHLORIDE ION × 10	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.5；291 K；35% (v/v) 2-methyl-2,4-pentanediol, 100 mM sodium acetate/acetic acid pH 4.5	Resolution 1.85 Å R-free 0.159
9NR3 CRBN-DDB1 in complex with GLUL-cN Deposited 2025-03-13	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 D 368–373（6 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；8% v/v TacsimateTM pH 6.0, 20% w/v Polyethylene glycol 3,350	Resolution 2.93 Å R-free 0.278
9OTM Human glutamine synthetase filament under turnover conditions Deposited 2025-05-27	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 20 PDB declaration: eicosameric	Chain A 1–373（373 aa） Chain B 1–373（373 aa） Chain C 1–373（373 aa） Chain D 1–373（373 aa） Chain E 1–373（373 aa） Chain F 1–373（373 aa） Chain G 1–373（373 aa） Chain H 1–373（373 aa） Chain I 1–373（373 aa） Chain J 1–373（373 aa） Chain K 1–373（373 aa） Chain L 1–373（373 aa） Chain M 1–373（373 aa） Chain N 1–373（373 aa） Chain O 1–373（373 aa） Chain P 1–373（373 aa） Chain Q 1–373（373 aa） Chain R 1–373（373 aa） Chain S 1–373（373 aa） Chain T 1–373（373 aa）	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 20 MG MAGNESIUM ION × 40 GLN GLUTAMINE × 5	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.19 Å
9OTN Human glutamine synthetase filament bound to ATP Deposited 2025-05-27	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 20 PDB declaration: eicosameric	Chain A 1–373（373 aa） Chain B 1–373（373 aa） Chain C 1–373（373 aa） Chain D 1–373（373 aa） Chain E 1–373（373 aa） Chain F 1–373（373 aa） Chain G 1–373（373 aa） Chain H 1–373（373 aa） Chain I 1–373（373 aa） Chain J 1–373（373 aa） Chain K 1–373（373 aa） Chain L 1–373（373 aa） Chain M 1–373（373 aa） Chain N 1–373（373 aa） Chain O 1–373（373 aa） Chain P 1–373（373 aa） Chain Q 1–373（373 aa） Chain R 1–373（373 aa） Chain S 1–373（373 aa） Chain T 1–373（373 aa）	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 20 MG MAGNESIUM ION × 40	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.11 Å
9OTO Human glutamine synthetase decamer under turnover conditions Deposited 2025-05-27	Different mutation/modification Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 10 PDB declaration: decameric	Chain A 1–373（373 aa） Chain B 1–373（373 aa） Chain C 1–373（373 aa） Chain D 1–373（373 aa） Chain E 1–373（373 aa） Chain F 1–373（373 aa） Chain G 1–373（373 aa） Chain H 1–373（373 aa） Chain I 1–373（373 aa） Chain J 1–373（373 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 10 MG MAGNESIUM ION × 20	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.03 Å
9OTQ Human glutamine synthetase filament apo Deposited 2025-05-27	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 20 PDB declaration: 20-meric	Chain L 1–373（373 aa） Chain M 1–373（373 aa） Chain N 1–373（373 aa） Chain O 1–373（373 aa） Chain P 1–373（373 aa） Chain Q 1–373（373 aa） Chain R 1–373（373 aa） Chain S 1–373（373 aa） Chain T 1–373（373 aa） Chain U 1–373（373 aa） Chain V 1–373（373 aa） Chain W 1–373（373 aa） Chain X 1–373（373 aa） Chain Y 1–373（373 aa） Chain Z 1–373（373 aa） Chain a 1–373（373 aa） Chain b 1–373（373 aa） Chain c 1–373（373 aa） Chain d 1–373（373 aa） Chain e 1–373（373 aa）	Not recorded	MG MAGNESIUM ION × 20	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.27 Å

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

View Construct and Data Evidence

UniProt name	GLNA_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–373； UniProt 1–373 Author chain B； PDBConstruct 1–373； UniProt 1–373 Author chain C； PDBConstruct 1–373； UniProt 1–373 Author chain D； PDBConstruct 1–373； UniProt 1–373 Author chain E； PDBConstruct 1–373； UniProt 1–373 Author chain F； PDBConstruct 1–373； UniProt 1–373 Author chain G； PDBConstruct 1–373； UniProt 1–373 Author chain H； PDBConstruct 1–373； UniProt 1–373 Author chain I； PDBConstruct 1–373； UniProt 1–373 Author chain J； PDBConstruct 1–373； UniProt 1–373

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	9otp
Deposition date deposition_date	2025-05-27
Structure title title	Human glutamine synthetase R298A decamer under turnover conditions
Keywords keywords	Glutamine synthetase, glutamate-ammonia ligase, Type II, LIGASE; LIGASE
Experimental Method method	ELECTRON MICROSCOPY

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

Radius of gyration Rg (Guinier) rg_guinier	48.40 Å
Radius of gyration Rg (electron density) rg_electron	47.60 Å
Forward intensity I(0) i0	2809080000.00
Molecular weight molecular_weight	422890.0 kDa
Excluded volume excluded_volume	519990 Å³
Envelope volume envelope_volume	696920 Å³
Hydration-shell volume shell_volume	114180 Å³
Envelope diameter envelope_diameter	146.3 Å
Shell Rg shell_rg	57.33 Å
Envelope Rg envelope_rg	46.87 Å
Shape Rg shape_rg	47.57 Å
Total Rg total_rg	47.99 Å
Total atoms total_atoms	57882
Residues n_residues	3721
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	134.4 Å
Rg (real space) rg_real	47.92 Å
Rg uncertainty (real space) rg_real_error	0.61 Å
I(0) (real space) i0_real	2.8090e+09
I(0) uncertainty (real space) i0_real_error	4.7840e+07
Rg (reciprocal space) rg_reciprocal	48.40 Å
I(0) (reciprocal space) i0_reciprocal	2811000000.0000
Solution quality estimate total_estimate	0.8483
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	65.2 Å
Skewness Skewness skewness	-0.002
Kurtosis Kurtosis kurtosis	-0.490
Angular range angular_range	— – 0.1650 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	356600000.0000
Real-space data points n_real_points	34
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.970; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.971; Smooth: 0.143

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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	Glutamine synthetase
Molecular weight formula_weight	42032.3 kDa
EC 编号 ec_number	6.3.1.2,2.3.1.225
Mutation mutation	R298A
Source method src_method	man
Copy count entity_count	10

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G,H,I,J
Atom count atom_count	57882

MTTSASSHLNKGIKQVYMSLPQGEKVQAMYIWIDGTGEGLRCKTRTLDSEPKCVEELPEWNFDGSSTLQSEGSNSDMYLVPAAMFRDPFRKDPNKLVLCEVFKYNRRPAETNLRHTCKRIMDMVSNQHPWFGMEQEYTLMGTDGHPFGWPSNGFPGPQGPYYCGVGADRAYGRDIVEAHYRACLYAGVKIAGTNAEVMPAQWEFQIGPCEGISMGDHLWVARFILHRVCEDFGVIATFDPKPIPGNWNGAGCHTNFSTKAMREENGLKYIEEAIEKLSKRHQYHIRAYDPKGGLDNAARLTGFHETSNINDFSAGVANRSASIRIPRTVGQEKKGYFEDRRPSANCDPFSVTEALIRTCLLNETGDEPFQYKN

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 BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	ADENOSINE-5'-DIPHOSPHATE
Molecular weight formula_weight	427.2 kDa
Source method src_method	syn
Copy count entity_count	10

Entity 3 Entity 3 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	20

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8. Citations (1)

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Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 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	—

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

Resolution resolution	1.95 Å
Resolution测定方法 resolution_method	—
颗粒数 num_particles	619435

fit	/app/data/saxs_computation/ot/9otp/9otp.fit
pddf	/app/data/pr_computation/ot/9otp/9otp.pr.out
profile	/app/data/saxs_computation/ot/9otp/9otp.dat

Human glutamine synthetase R298A decamer under turnover conditions

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

Glutamine synthetase

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

冷冻电镜 EM 3D