7dpt

Structural basis for ligand binding modes of CTP synthase

Method: ELECTRON MICROSCOPY

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

CTP synthase

Drosophila melanogaster

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 4	GUANOSINE-5'-TRIPHOSPHATE × 4 6-DIAZENYL-5-OXO-L-NORLEUCINE × 4 ADENOSINE-5'-DIPHOSPHATE × 4 MAGNESIUM ION × 12 ;[[(2~{R},3~{S},4~{R},5~{R})-3,4-bis(oxidanyl)-5-(2-oxidanyl-4-phosphonooxy-pyrimidin-1-yl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate ; × 4 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PYRG_DROME
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–627； UniProt 1–627 Author chain B； PDBConstruct 1–627； UniProt 1–627 Author chain C； PDBConstruct 1–627； UniProt 1–627 Author chain D； PDBConstruct 1–627； UniProt 1–627

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	7dpt
Deposition date deposition_date	2020-12-21
Structure title title	Structural basis for ligand binding modes of CTP synthase
Keywords keywords	substrate-bound, filament, LIGASE, DON; LIGASE
Experimental Method method	ELECTRON MICROSCOPY

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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.

7dpt__assembly_1__model_1

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

Download this curve (.dat)

7dpt__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

7dpt__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	43.87 Å
Rg (electron density)	43.60 Å
Total Rg	43.64 Å
Atom count	17956
Residues	2224
Excluded volume	319040 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`7dpt__assembly_1__model_1`	tetrameric （4）	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 (7)

Entity 1 Entity 1 polymer

Description description	CTP synthase
Molecular weight formula_weight	69539.5 kDa
EC 编号 ec_number	6.3.4.2
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	18052

MKYILVTGGVISGVGKGVIASSFGTLLKSCGLDVTSIKIDPYINIDAGTFSPYEHGEVYVLDDGAEVDLDLGNYERFLDVTLHRDNNITTGKIYKLVIEKERTGEYLGKTVQVVPHITDAIQEWVERVAQTPVQGSSKPQVCIVELGGTIGDIEGMPFVEAFRQFQFRVKRENFCLAHVSLVPLPKATGEPKTKPTQSSVRELRGCGLSPDLIVCRSEKPIGLEVKEKISNFCHVGPDQVICIHDLNSIYHVPLLMEQNGVIEYLNERLQLNIDMSKRTKCLQQWRDLARRTETVRREVCIAVVGKYTKFTDSYASVVKALQHAALAVNRKLELVFIESCLLEEETLHSEPSKYHKEWQKLCDSHGILVPGGFGSRGMEGKIRACQWARENQKPLLGICLGLQAAVIEFARNKLGLKDANTTEIDPNTANALVIDMPEHHTGQLGGTMRLGKRITVFSDGPSVIRQLYGNPKSVQERHRHRYEVNPKYVHLLEEQGMRFVGTDVDKTRMEIIELSGHPYFVATQYHPEYLSRPLKPSPPFLGLILASVDRLNQYIQRGCRLSPRQLSDASSDEEDSVVGLAGATKSLSSLKIPITPTNGISKSCNGSISTSDSEGACGGVDPTNGHK

Source Source

Source organism organism	Drosophila melanogaster
Common name common_name	Fruit fly
NCBI taxonomy ID ncbi_taxonomy_id	7227
Host organism host_organism	;Escherichia coli 'BL21-Gold(DE3)pLysS AG' ;

Entity 2 Entity 2 non-polymer

Description description	GUANOSINE-5'-TRIPHOSPHATE
Molecular weight formula_weight	523.2 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 non-polymer

Description description	6-DIAZENYL-5-OXO-L-NORLEUCINE
Molecular weight formula_weight	173.2 kDa
Source method src_method	syn
Copy count entity_count	4

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	4

Entity 5 Entity 5 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	12

Entity 6 Entity 6 non-polymer

Description description	;[[(2~{R},3~{S},4~{R},5~{R})-3,4-bis(oxidanyl)-5-(2-oxidanyl-4-phosphonooxy-pyrimidin-1-yl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate ;
Molecular weight formula_weight	565.1 kDa
Source method src_method	nat
Copy count entity_count	4

Entity 7 Entity 7 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	96

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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	triclinic

Resolution resolution	2.48 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	107556

Structural basis for ligand binding modes of CTP synthase

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

CTP synthase

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

7dpt__assembly_1__model_1

7dpt__assembly_1__model_1 | I(q)

7dpt__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (7)

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 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

7. Citations (1)

Structural basis for ligand binding modes of CTP synthase

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

CTP synthase

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

7dpt__assembly_1__model_1

7dpt__assembly_1__model_1 | I(q)

7dpt__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (7)

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 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

7. Citations (1)