2d3c

Crystal Structure of the Maize Glutamine Synthetase complexed with ADP and Phosphinothricin Phosphate

Method: X-RAY DIFFRACTION

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

glutamine synthetase

Zea mays

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 10	MANGANESE (II) ION × 30 (2S)-2-AMINO-4-[METHYL(PHOSPHONOOXY)PHOSPHORYL]BUTANOIC ACID × 10 ADENOSINE-5'-DIPHOSPHATE × 10 water × 10	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	GLNA3_MAIZE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–356； UniProt 1–356 Author chain B； PDBConstruct 1–356； UniProt 1–356 Author chain C； PDBConstruct 1–356； UniProt 1–356 Author chain D； PDBConstruct 1–356； UniProt 1–356 Author chain E； PDBConstruct 1–356； UniProt 1–356 Author chain F； PDBConstruct 1–356； UniProt 1–356 Author chain G； PDBConstruct 1–356； UniProt 1–356 Author chain H； PDBConstruct 1–356； UniProt 1–356 Author chain I； PDBConstruct 1–356； UniProt 1–356 Author chain J； PDBConstruct 1–356； UniProt 1–356

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	2d3c
Deposition date deposition_date	2005-09-26
Structure title title	Crystal Structure of the Maize Glutamine Synthetase complexed with ADP and Phosphinothricin Phosphate
Keywords keywords	GLUTAMINE SYNTHETASE MAIZE HERBICIDE, LIGASE; 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.

2d3c__assembly_1__model_1

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

Download this curve (.dat)

2d3c__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2d3c__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	47.12 Å
Rg (electron density)	46.42 Å
Total Rg	46.71 Å
Atom count	27900
Residues	3530
Excluded volume	491670 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2d3c__assembly_1__model_1`	decameric （10）	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 (5)

Entity 1 Entity 1 polymer

Description description	glutamine synthetase
Molecular weight formula_weight	39264.0 kDa
EC 编号 ec_number	6.3.1.2
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	28138

MACLTDLVNLNLSDTTEKIIAEYIWIGGSGMDLRSKARTLPGPVTDPSKLPKWNYDGSSTGQAPGEDSEVILYPQAIFKDPFRRGNNILVMCDCYTPAGEPIPTNKRYSAAKIFSSPEVAAEEPWYGIEQEYTLLQKDTNWPLGWPIGGFPGPQGPYYCGIGAEKSFGRDIVDAHYKACLYAGINISGINGEVMPGQWEFQVGPSVGISSGDQVWVARYILERITEIAGVVVTFDPKPIPGDWNGAGAHTNYSTESMRKEGGYEVIKAAIEKLKLRHKEHIAAYGEGNERRLTGRHETADINTFSWGVANRGASVRVGRETEQNGKGYFEDRRPASNMDPYVVTSMIAETTIVWKP

Source Source

Source organism organism	Zea mays
NCBI taxonomy ID ncbi_taxonomy_id	4577
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	MANGANESE (II) ION
Molecular weight formula_weight	54.9 kDa
Source method src_method	syn
Copy count entity_count	30

Entity 3 Entity 3 non-polymer

Description description	(2S)-2-AMINO-4-[METHYL(PHOSPHONOOXY)PHOSPHORYL]BUTANOIC ACID
Molecular weight formula_weight	261.1 kDa
Source method src_method	syn
Copy count entity_count	10

Entity 4 Entity 4 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 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	238

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6. Fold Classification (SCOP + CATH) 20 domains

CATH v4.4 (20 domains)

Domain ID domain_id	2d3cA01
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily	70 — Glutamine synthetase, N-terminal domain

Domain ID domain_id	2d3cA02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	590 — Creatine Kinase; Chain A, domain 2
Homologous superfamily homologous superfamily	10 — Glutamine synthetase/guanido kinase, catalytic domain

Domain ID domain_id	2d3cB01
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily	70 — Glutamine synthetase, N-terminal domain

Domain ID domain_id	2d3cB02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	590 — Creatine Kinase; Chain A, domain 2
Homologous superfamily homologous superfamily	10 — Glutamine synthetase/guanido kinase, catalytic domain

Domain ID domain_id	2d3cC01
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily	70 — Glutamine synthetase, N-terminal domain

Domain ID domain_id	2d3cC02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	590 — Creatine Kinase; Chain A, domain 2
Homologous superfamily homologous superfamily	10 — Glutamine synthetase/guanido kinase, catalytic domain

Domain ID domain_id	2d3cD01
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily	70 — Glutamine synthetase, N-terminal domain

Domain ID domain_id	2d3cD02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	590 — Creatine Kinase; Chain A, domain 2
Homologous superfamily homologous superfamily	10 — Glutamine synthetase/guanido kinase, catalytic domain

Domain ID domain_id	2d3cE01
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily	70 — Glutamine synthetase, N-terminal domain

Domain ID domain_id	2d3cE02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	590 — Creatine Kinase; Chain A, domain 2
Homologous superfamily homologous superfamily	10 — Glutamine synthetase/guanido kinase, catalytic domain

Domain ID domain_id	2d3cF01
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily	70 — Glutamine synthetase, N-terminal domain

Domain ID domain_id	2d3cF02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	590 — Creatine Kinase; Chain A, domain 2
Homologous superfamily homologous superfamily	10 — Glutamine synthetase/guanido kinase, catalytic domain

Domain ID domain_id	2d3cG01
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily	70 — Glutamine synthetase, N-terminal domain

Domain ID domain_id	2d3cG02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	590 — Creatine Kinase; Chain A, domain 2
Homologous superfamily homologous superfamily	10 — Glutamine synthetase/guanido kinase, catalytic domain

Domain ID domain_id	2d3cH01
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily	70 — Glutamine synthetase, N-terminal domain

Domain ID domain_id	2d3cH02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	590 — Creatine Kinase; Chain A, domain 2
Homologous superfamily homologous superfamily	10 — Glutamine synthetase/guanido kinase, catalytic domain

Domain ID domain_id	2d3cI01
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily	70 — Glutamine synthetase, N-terminal domain

Domain ID domain_id	2d3cI02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	590 — Creatine Kinase; Chain A, domain 2
Homologous superfamily homologous superfamily	10 — Glutamine synthetase/guanido kinase, catalytic domain

Domain ID domain_id	2d3cJ01
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily	70 — Glutamine synthetase, N-terminal domain

Domain ID domain_id	2d3cJ02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	590 — Creatine Kinase; Chain A, domain 2
Homologous superfamily homologous superfamily	10 — Glutamine synthetase/guanido kinase, catalytic domain

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Unit-cell length a length_a	95.958 Å
Unit-cell length b length_b	191.012 Å
Unit-cell length c length_c	118.124 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	101.23 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	20

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	3.810 Å
Low-resolution limit resolution_low	27.360 Å
R factor r_factor	0.1869
R_work r_work	0.1846
R_free r_free	0.2294

Crystal Structure of the Maize Glutamine Synthetase complexed with ADP and Phosphinothricin Phosphate

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

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

2d3c__assembly_1__model_1

2d3c__assembly_1__model_1 | I(q)

2d3c__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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 20 domains

CATH v4.4 (20 domains)

7. Citations (1)

Crystal Structure of the Maize Glutamine Synthetase complexed with ADP and Phosphinothricin Phosphate

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

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

2d3c__assembly_1__model_1

2d3c__assembly_1__model_1 | I(q)

2d3c__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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 20 domains

CATH v4.4 (20 domains)

7. Citations (1)