1fpy

CRYSTAL STRUCTURE OF GLUTAMINE SYNTHETASE FROM SALMONELLA TYPHIMURIUM WITH INHIBITOR PHOSPHINOTHRICIN

Method: X-RAY DIFFRACTION

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

GLUTAMINE SYNTHETASE

Salmonella typhimurium

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 12	MANGANESE (II) ION × 24 ADENOSINE-5'-DIPHOSPHATE × 12 PHOSPHINOTHRICIN × 12 water × 12	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	GLNA_SALTY
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–468； UniProt 1–468 Author chain B； PDBConstruct 1–468； UniProt 1–468 Author chain C； PDBConstruct 1–468； UniProt 1–468 Author chain D； PDBConstruct 1–468； UniProt 1–468 Author chain E； PDBConstruct 1–468； UniProt 1–468 Author chain F； PDBConstruct 1–468； UniProt 1–468 Author chain G； PDBConstruct 1–468； UniProt 1–468 Author chain H； PDBConstruct 1–468； UniProt 1–468 Author chain I； PDBConstruct 1–468； UniProt 1–468 Author chain J； PDBConstruct 1–468； UniProt 1–468 Author chain K； PDBConstruct 1–468； UniProt 1–468 Author chain L； PDBConstruct 1–468； UniProt 1–468

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	1fpy
Deposition date deposition_date	2000-08-31
Structure title title	CRYSTAL STRUCTURE OF GLUTAMINE SYNTHETASE FROM SALMONELLA TYPHIMURIUM WITH INHIBITOR PHOSPHINOTHRICIN
Keywords keywords	glutamine synthetase, phosphinothricin, inhibition, 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.

1fpy__assembly_1__model_1

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

Download this curve (.dat)

1fpy__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1fpy__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	54.43 Å
Rg (electron density)	53.98 Å
Total Rg	54.35 Å
Atom count	44124
Residues	5616
Excluded volume	780170 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1fpy__assembly_1__model_1`	dodecameric （12）	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	51744.4 kDa
EC 编号 ec_number	6.3.1.2
Source method src_method	man
Copy count entity_count	12

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G,H,I,J,K,L
Atom count atom_count	47280

SAEHVLTMLNEHEVKFVDLRFTDTKGKEQHVTIPAHQVNAEFFEEGKMFDGSSIGGWKGINESDMVLMPDASTAVIDPFFADSTLIIRCDILEPGTLQGYDRDPRSIAKRAEDYLRATGIADTVLFGPEPEFFLFDDIRFGASISGSHVAIDDIEGAWNSSTKYEGGNKGHRPGVKGGYFPVPPVDSAQDIRSEMCLVMEQMGLVVEAHHHEVATAGQNEVATRFNTMTKKADEIQIYKYVVHNVAHRFGKTATFMPKPMFGDNGSGMHCHMSLAKNGTNLFSGDKYAGLSEQALYYIGGVIKHAKAINALANPTTNSYKRLVPGYEAPVMLAYSARNRSASIRIPVVASPKARRIEVRFPDPAANPYLCFAALLMAGLDGIKNKIHPGEPMDKNLYDLPPEEAKEIPQVAGSLEEALNALDLDREFLKAGGVFTDEAIDAYIALRREEDDRVRMTPHPVEFELYYSV

Source Source

Source organism organism	Salmonella typhimurium
NCBI taxonomy ID ncbi_taxonomy_id	602
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	24

Entity 3 Entity 3 non-polymer

Description description	ADENOSINE-5'-DIPHOSPHATE
Molecular weight formula_weight	427.2 kDa
Source method src_method	syn
Copy count entity_count	12

Entity 4 Entity 4 non-polymer

Description description	PHOSPHINOTHRICIN
Molecular weight formula_weight	181.1 kDa
Source method src_method	syn
Copy count entity_count	12

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1836

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6. Fold Classification (SCOP + CATH) 48 domains

SCOP 2.08 (24 domains)

Domain ID domain_id	d1fpya1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.15 — beta-Grasp (ubiquitin-like)
Superfamily Superfamily superfamily	d.15.9 — Glutamine synthetase, N-terminal domain
Family Family family	d.15.9.1 — Glutamine synthetase, N-terminal domain

Domain ID domain_id	d1fpya2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.128 — Glutamine synthetase/guanido kinase
Superfamily Superfamily superfamily	d.128.1 — Glutamine synthetase/guanido kinase
Family Family family	d.128.1.1 — Glutamine synthetase catalytic domain

Domain ID domain_id	d1fpyb1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.15 — beta-Grasp (ubiquitin-like)
Superfamily Superfamily superfamily	d.15.9 — Glutamine synthetase, N-terminal domain
Family Family family	d.15.9.1 — Glutamine synthetase, N-terminal domain

Domain ID domain_id	d1fpyb2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.128 — Glutamine synthetase/guanido kinase
Superfamily Superfamily superfamily	d.128.1 — Glutamine synthetase/guanido kinase
Family Family family	d.128.1.1 — Glutamine synthetase catalytic domain

Domain ID domain_id	d1fpyc1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.15 — beta-Grasp (ubiquitin-like)
Superfamily Superfamily superfamily	d.15.9 — Glutamine synthetase, N-terminal domain
Family Family family	d.15.9.1 — Glutamine synthetase, N-terminal domain

Domain ID domain_id	d1fpyc2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.128 — Glutamine synthetase/guanido kinase
Superfamily Superfamily superfamily	d.128.1 — Glutamine synthetase/guanido kinase
Family Family family	d.128.1.1 — Glutamine synthetase catalytic domain

Domain ID domain_id	d1fpyd1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.15 — beta-Grasp (ubiquitin-like)
Superfamily Superfamily superfamily	d.15.9 — Glutamine synthetase, N-terminal domain
Family Family family	d.15.9.1 — Glutamine synthetase, N-terminal domain

Domain ID domain_id	d1fpyd2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.128 — Glutamine synthetase/guanido kinase
Superfamily Superfamily superfamily	d.128.1 — Glutamine synthetase/guanido kinase
Family Family family	d.128.1.1 — Glutamine synthetase catalytic domain

Domain ID domain_id	d1fpye1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.15 — beta-Grasp (ubiquitin-like)
Superfamily Superfamily superfamily	d.15.9 — Glutamine synthetase, N-terminal domain
Family Family family	d.15.9.1 — Glutamine synthetase, N-terminal domain

Domain ID domain_id	d1fpye2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.128 — Glutamine synthetase/guanido kinase
Superfamily Superfamily superfamily	d.128.1 — Glutamine synthetase/guanido kinase
Family Family family	d.128.1.1 — Glutamine synthetase catalytic domain

Domain ID domain_id	d1fpyf1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.15 — beta-Grasp (ubiquitin-like)
Superfamily Superfamily superfamily	d.15.9 — Glutamine synthetase, N-terminal domain
Family Family family	d.15.9.1 — Glutamine synthetase, N-terminal domain

Domain ID domain_id	d1fpyf2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.128 — Glutamine synthetase/guanido kinase
Superfamily Superfamily superfamily	d.128.1 — Glutamine synthetase/guanido kinase
Family Family family	d.128.1.1 — Glutamine synthetase catalytic domain

Domain ID domain_id	d1fpyg1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.15 — beta-Grasp (ubiquitin-like)
Superfamily Superfamily superfamily	d.15.9 — Glutamine synthetase, N-terminal domain
Family Family family	d.15.9.1 — Glutamine synthetase, N-terminal domain

Domain ID domain_id	d1fpyg2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.128 — Glutamine synthetase/guanido kinase
Superfamily Superfamily superfamily	d.128.1 — Glutamine synthetase/guanido kinase
Family Family family	d.128.1.1 — Glutamine synthetase catalytic domain

Domain ID domain_id	d1fpyh1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.15 — beta-Grasp (ubiquitin-like)
Superfamily Superfamily superfamily	d.15.9 — Glutamine synthetase, N-terminal domain
Family Family family	d.15.9.1 — Glutamine synthetase, N-terminal domain

Domain ID domain_id	d1fpyh2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.128 — Glutamine synthetase/guanido kinase
Superfamily Superfamily superfamily	d.128.1 — Glutamine synthetase/guanido kinase
Family Family family	d.128.1.1 — Glutamine synthetase catalytic domain

Domain ID domain_id	d1fpyi1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.15 — beta-Grasp (ubiquitin-like)
Superfamily Superfamily superfamily	d.15.9 — Glutamine synthetase, N-terminal domain
Family Family family	d.15.9.1 — Glutamine synthetase, N-terminal domain

Domain ID domain_id	d1fpyi2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.128 — Glutamine synthetase/guanido kinase
Superfamily Superfamily superfamily	d.128.1 — Glutamine synthetase/guanido kinase
Family Family family	d.128.1.1 — Glutamine synthetase catalytic domain

Domain ID domain_id	d1fpyj1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.15 — beta-Grasp (ubiquitin-like)
Superfamily Superfamily superfamily	d.15.9 — Glutamine synthetase, N-terminal domain
Family Family family	d.15.9.1 — Glutamine synthetase, N-terminal domain

Domain ID domain_id	d1fpyj2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.128 — Glutamine synthetase/guanido kinase
Superfamily Superfamily superfamily	d.128.1 — Glutamine synthetase/guanido kinase
Family Family family	d.128.1.1 — Glutamine synthetase catalytic domain

Domain ID domain_id	d1fpyk1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.15 — beta-Grasp (ubiquitin-like)
Superfamily Superfamily superfamily	d.15.9 — Glutamine synthetase, N-terminal domain
Family Family family	d.15.9.1 — Glutamine synthetase, N-terminal domain

Domain ID domain_id	d1fpyk2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.128 — Glutamine synthetase/guanido kinase
Superfamily Superfamily superfamily	d.128.1 — Glutamine synthetase/guanido kinase
Family Family family	d.128.1.1 — Glutamine synthetase catalytic domain

Domain ID domain_id	d1fpyl1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.15 — beta-Grasp (ubiquitin-like)
Superfamily Superfamily superfamily	d.15.9 — Glutamine synthetase, N-terminal domain
Family Family family	d.15.9.1 — Glutamine synthetase, N-terminal domain

Domain ID domain_id	d1fpyl2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.128 — Glutamine synthetase/guanido kinase
Superfamily Superfamily superfamily	d.128.1 — Glutamine synthetase/guanido kinase
Family Family family	d.128.1.1 — Glutamine synthetase catalytic domain

CATH v4.4 (24 domains)

Domain ID domain_id	1fpyA01
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	1fpyA02
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	1fpyB01
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	1fpyB02
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	1fpyC01
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	1fpyC02
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	1fpyD01
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	1fpyD02
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	1fpyE01
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	1fpyE02
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	1fpyF01
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	1fpyF02
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	1fpyG01
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	1fpyG02
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	1fpyH01
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	1fpyH02
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	1fpyI01
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	1fpyI02
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	1fpyJ01
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	1fpyJ02
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	1fpyK01
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	1fpyK02
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	1fpyL01
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	1fpyL02
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

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Unit-cell length a length_a	230.600 Å
Unit-cell length b length_b	132.500 Å
Unit-cell length c length_c	195.900 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	102.40 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	48

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	2.890 Å
Low-resolution limit resolution_low	15.000 Å
R factor r_factor	0.2500
R_work r_work	0.2480
R_free r_free	0.2630

CRYSTAL STRUCTURE OF GLUTAMINE SYNTHETASE FROM SALMONELLA TYPHIMURIUM WITH INHIBITOR PHOSPHINOTHRICIN

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

1fpy__assembly_1__model_1

1fpy__assembly_1__model_1 | I(q)

1fpy__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) 48 domains

SCOP 2.08 (24 domains)

CATH v4.4 (24 domains)

7. Citations (1)

CRYSTAL STRUCTURE OF GLUTAMINE SYNTHETASE FROM SALMONELLA TYPHIMURIUM WITH INHIBITOR PHOSPHINOTHRICIN

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

1fpy__assembly_1__model_1

1fpy__assembly_1__model_1 | I(q)

1fpy__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) 48 domains

SCOP 2.08 (24 domains)

CATH v4.4 (24 domains)

7. Citations (1)