SAXSdb — 2vpm

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

TRYPANOTHIONE SYNTHETASE

LEISHMANIA MAJOR

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	CHLORIDE ION × 5 BROMIDE ION × 1 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	CHLORIDE ION × 3 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q711P7_LEIMA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–653； UniProt 1–652 Author chain B； PDBConstruct 2–653； UniProt 1–652

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	2vpm
Deposition date deposition_date	2008-03-03
Structure title title	Trypanothione synthetase
Keywords keywords	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.

2vpm__assembly_1__model_1

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

Download this curve (.dat)

2vpm__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2vpm__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	28.01 Å
Rg (electron density)	26.99 Å
Total Rg	27.89 Å
Atom count	4871
Residues	600
Excluded volume	86179 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2vpm__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2vpm__assembly_2__model_1`	monomeric （1）	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 (4)

Entity 1 Entity 1 polymer

Description description	TRYPANOTHIONE SYNTHETASE
Molecular weight formula_weight	74668.2 kDa
EC 编号 ec_number	6.3.1.9
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	9867

HMSSLQRASVSFNKPGHIPFGAVQGYAPGGVPAYSNKHDHYFSGERNIEDNIFFGFKYQCVEFARRWLLVRKGLLLPDVNWACHIFQLKEVRDAATTESFAVLQVRNGTTTKPEADALLVYPSTDANPVGHVGTITEVGDDYVCVADQNYRFHKWESSCAYKLKLDHRDGIWTIIDDIDADEIEIPLGWLTFPGRANRPEGAPPVALHPSLHFKEPPKPYLLRRNFLPTESKANWLDMNNPAERLFVEEFGMDVSRTRLEEKVVSYYESNHEFHLRCVAYGTQLHAIFMEATAQVIESDEKLRLFAIPEEFWPRIRHSWKYQQTYISGRFDFAFNNETGEVKCFEYNADSASTLLECGLIQQKWAESVGLDKQDTRGSGFAVERNLKMAWANSGATGRVHFCVDEEREEQYTALYCMQAAEAVGLEGKLCILFDEFRFDDNGHVVDSDGVRVRNVWKTWMWESAITDYYAAREERGENWKPSPKDKVRLCDLLLGDDWEILYFEPMWKVIPSNKAILPMIYHNHPEHPAILKAEYELTDELRKHGYAKKPIVGRVGSNVIITSGDGVVHAESGGKYGKRNMIYQQLFELKKQDDYYAIIGGWMIGDAFSGTGIREDKSVITGVDSPFAAVRIKTDKLPHPVTLKDIDKMAEDE

Source Source

Source organism organism	LEISHMANIA MAJOR
NCBI taxonomy ID ncbi_taxonomy_id	5664
Host organism host_organism	ESCHERICHIA COLI

Entity 2 Entity 2 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	8

Entity 3 Entity 3 non-polymer

Description description	BROMIDE ION
Molecular weight formula_weight	79.9 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	161

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6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	2vpmA01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	1720 — endopeptidase fold (from Nostoc punctiforme)
Homologous superfamily homologous superfamily	10 — endopeptidase domain like (from Nostoc punctiforme)

Domain ID domain_id	2vpmB01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	1720 — endopeptidase fold (from Nostoc punctiforme)
Homologous superfamily homologous superfamily	10 — endopeptidase domain like (from Nostoc punctiforme)

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Unit-cell length a length_a	70.522 Å
Unit-cell length b length_b	167.082 Å
Unit-cell length c length_c	84.921 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	94.11 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

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

Resolution resolution	2.800 Å
Low-resolution limit resolution_low	84.820 Å
R factor r_factor	0.2050
R_work r_work	0.2030
R_free r_free	0.2530

Trypanothione synthetase

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

TRYPANOTHIONE 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

2vpm__assembly_1__model_1

2vpm__assembly_1__model_1 | I(q)

2vpm__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 (4)

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 water

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)

Trypanothione synthetase

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

TRYPANOTHIONE 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

2vpm__assembly_1__model_1

2vpm__assembly_1__model_1 | I(q)

2vpm__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 (4)

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 water

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)