2ojw

Crystal structure of human glutamine synthetase in complex with ADP and phosphate

Method: X-RAY DIFFRACTION Dmax: 125.9 Å Quality: EXCELLENT

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

Glutamine synthetase

Homo sapiens

UniProt P15104

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 4–364 Chain B; UniProt 4–364 Chain C; UniProt 4–364 Chain D; UniProt 4–364 Chain E; UniProt 4–364 Fragment:Residues 4-364 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

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.

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 24–384; UniProt 4–364 Author chain B; PDBConstruct 24–384; UniProt 4–364 Author chain C; PDBConstruct 24–384; UniProt 4–364 Author chain D; PDBConstruct 24–384; UniProt 4–364 Author chain E; PDBConstruct 24–384; UniProt 4–364

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.

SAXS scattering curve SAXS Profile

SAXS profile for 2ojw

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 2ojw
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2. Structure Basics 2. Structure Basics

Entry ID entry_id2ojw
Deposition date deposition_date2007-01-15
Structure title titleCrystal structure of human glutamine synthetase in complex with ADP and phosphate
Keywords keywordsAMINO-ACID BIOSYNTHESIS, LIGASE, SYNTHETASE, STRUCTURAL GENOMICS, Structural Genomics Consortium, SGC; LIGASE
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier39.99
Radius of gyration Rg (electron density) rg_electron39.38
Forward intensity I(0) i0709028000.00
Molecular weight molecular_weight207310.0 kDa
Excluded volume excluded_volume254010 ų
Envelope volume envelope_volume316190 ų
Hydration-shell volume shell_volume64001 ų
Envelope diameter envelope_diameter126.3
Shell Rg shell_rg47.25
Envelope Rg envelope_rg39.30
Shape Rg shape_rg39.38
Total Rg total_rg39.75
Total atoms total_atoms14471
Residues n_residues1802
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 −1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3

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

Maximum dimension Dmax dmax125.9
Rg (real space) rg_real39.89
Rg uncertainty (real space) rg_real_error0.78
I(0) (real space) i0_real7.0900e+08
I(0) uncertainty (real space) i0_real_error1.1140e+07
Rg (reciprocal space) rg_reciprocal39.99
I(0) (reciprocal space) i0_reciprocal709100000.0000
Solution quality estimate total_estimate0.9029
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary50.4
Skewness Skewness skewness0.171
Kurtosis Kurtosis kurtosis-0.652
Angular range angular_range— – 0.2000 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha250600000.0000
Real-space data points n_real_points41
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.952; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.878

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (7)

7. Fold Classification (SCOP + CATH) 10 domains

CATH v4.4 (10 domains)

Domain ID domain_id2ojwA01
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily70 — Glutamine synthetase, N-terminal domain
Domain ID domain_id2ojwA02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology590 — Creatine Kinase; Chain A, domain 2
Homologous superfamily homologous superfamily10 — Glutamine synthetase/guanido kinase, catalytic domain
Domain ID domain_id2ojwB01
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily70 — Glutamine synthetase, N-terminal domain
Domain ID domain_id2ojwB02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology590 — Creatine Kinase; Chain A, domain 2
Homologous superfamily homologous superfamily10 — Glutamine synthetase/guanido kinase, catalytic domain
Domain ID domain_id2ojwC01
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily70 — Glutamine synthetase, N-terminal domain
Domain ID domain_id2ojwC02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology590 — Creatine Kinase; Chain A, domain 2
Homologous superfamily homologous superfamily10 — Glutamine synthetase/guanido kinase, catalytic domain
Domain ID domain_id2ojwD01
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily70 — Glutamine synthetase, N-terminal domain
Domain ID domain_id2ojwD02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology590 — Creatine Kinase; Chain A, domain 2
Homologous superfamily homologous superfamily10 — Glutamine synthetase/guanido kinase, catalytic domain
Domain ID domain_id2ojwE01
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily70 — Glutamine synthetase, N-terminal domain
Domain ID domain_id2ojwE02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology590 — Creatine Kinase; Chain A, domain 2
Homologous superfamily homologous superfamily10 — Glutamine synthetase/guanido kinase, catalytic domain

8. Citations (1)

9. Files and Curves (10)