3dmt

Structure of Glycosomal Glyceraldehyde-3-Phosphate Dehydrogenase from Trypanosoma cruzi in complex with the irreversible iodoacetate inhibitor

Method: X-RAY DIFFRACTION

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

Glyceraldehyde-3-phosphate dehydrogenase, glycosomal

Trypanosoma cruzi

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 4	NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 4 GLYCEROL × 1 water × 4	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 2 water × 2	Consistent with protein count
3	Protein homooligomer	Homooligomer	Protein 2	NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 2 GLYCEROL × 1 water × 2	Consistent with protein count
4	Protein homooligomer	Homooligomer	Protein 2	NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 2 water × 2	Consistent with protein count
5	Protein homooligomer	Homooligomer	Protein 2	NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 2 GLYCEROL × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	G3PG_TRYCR
Isoform	—
PDB entities	1, 2
Chains and sequence ranges	Author chain A； PDBConstruct 1–359； UniProt 1–359 Author chain B； PDBConstruct 1–359； UniProt 1–359 Author chain D； PDBConstruct 1–359； UniProt 1–359 Author chain C； PDBConstruct 1–359； UniProt 1–359

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	3dmt
Deposition date deposition_date	2008-07-01
Structure title title	Structure of Glycosomal Glyceraldehyde-3-Phosphate Dehydrogenase from Trypanosoma cruzi in complex with the irreversible iodoacetate inhibitor
Keywords keywords	ACTIVE-SITE CARBOXYMETHYLATION, IRREVERSIBLE INHIBITOR COMPLEX, TRYPANOSOMA CRUZI, Glycolysis, Glycosome, NAD, Oxidoreductase; OXIDOREDUCTASE
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.

3dmt__assembly_1__model_1

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

Download this curve (.dat)

3dmt__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3dmt__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	32.85 Å
Rg (electron density)	31.92 Å
Total Rg	32.58 Å
Atom count	11118
Residues	1435
Excluded volume	196870 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3dmt__assembly_1__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3dmt__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`3dmt__assembly_3__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`3dmt__assembly_4__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
5	1	`3dmt__assembly_5__model_1`	dimeric （2）	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	Glyceraldehyde-3-phosphate dehydrogenase, glycosomal
Molecular weight formula_weight	39112.5 kDa
EC 编号 ec_number	1.2.1.12
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,D
Atom count atom_count	12123

MPIKVGINGFGRIGRMVFQALCEDGLLGTEIDVVAVVDMNTDAEYFAYQMRYDTVHGKFKYEVTTTKSSPSVAKDDTLVVNGHRILCVKAQRNPADLPWGKLGVEYVIESTGLFTAKAAAEGHLRGGARKVVISAPASGGAKTLVMGVNHHEYNPSEHHVVSNASCTTNCLAPIVHVLVKEGFGVQTGLMTTIHSYTATQKTVDGVSVKDWRGGRAAAVNIIPSTTGAAKAVGMVIPSTQGKLTGMSFRVPTPDVSVVDLTFTAARDTSIQEIDAALKRASKTYMKGILGYTDEELVSADFINDNRSSIYDSKATLQNNLPKERRFFKIVSWYDNEWGYSHRVVDLVRHMASKDRSARL

Source Source

Source organism organism	Trypanosoma cruzi
NCBI taxonomy ID ncbi_taxonomy_id	5693
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Glyceraldehyde-3-phosphate dehydrogenase, glycosomal
Molecular weight formula_weight	39170.6 kDa
EC 编号 ec_number	1.2.1.12
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

Source Source

Source organism organism	Trypanosoma cruzi
NCBI taxonomy ID ncbi_taxonomy_id	5693
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 non-polymer

Description description	NICOTINAMIDE-ADENINE-DINUCLEOTIDE
Molecular weight formula_weight	663.4 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 4 Entity 4 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1005

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6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

Domain ID domain_id	d3dmta1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.2 — NAD(P)-binding Rossmann-fold domains
Superfamily Superfamily superfamily	c.2.1 — NAD(P)-binding Rossmann-fold domains
Family Family family	c.2.1.3 — Glyceraldehyde-3-phosphate dehydrogenase-like, N-terminal domain

Domain ID domain_id	d3dmta2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.81 — FwdE/GAPDH domain-like
Superfamily Superfamily superfamily	d.81.1 — Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain
Family Family family	d.81.1.1 — GAPDH-like

Domain ID domain_id	d3dmtb1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.2 — NAD(P)-binding Rossmann-fold domains
Superfamily Superfamily superfamily	c.2.1 — NAD(P)-binding Rossmann-fold domains
Family Family family	c.2.1.3 — Glyceraldehyde-3-phosphate dehydrogenase-like, N-terminal domain

Domain ID domain_id	d3dmtb2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.81 — FwdE/GAPDH domain-like
Superfamily Superfamily superfamily	d.81.1 — Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain
Family Family family	d.81.1.1 — GAPDH-like

Domain ID domain_id	d3dmtc1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.2 — NAD(P)-binding Rossmann-fold domains
Superfamily Superfamily superfamily	c.2.1 — NAD(P)-binding Rossmann-fold domains
Family Family family	c.2.1.3 — Glyceraldehyde-3-phosphate dehydrogenase-like, N-terminal domain

Domain ID domain_id	d3dmtc2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.81 — FwdE/GAPDH domain-like
Superfamily Superfamily superfamily	d.81.1 — Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain
Family Family family	d.81.1.1 — GAPDH-like

Domain ID domain_id	d3dmtd1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.2 — NAD(P)-binding Rossmann-fold domains
Superfamily Superfamily superfamily	c.2.1 — NAD(P)-binding Rossmann-fold domains
Family Family family	c.2.1.3 — Glyceraldehyde-3-phosphate dehydrogenase-like, N-terminal domain

Domain ID domain_id	d3dmtd2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.81 — FwdE/GAPDH domain-like
Superfamily Superfamily superfamily	d.81.1 — Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain
Family Family family	d.81.1.1 — GAPDH-like

CATH v4.4 (8 domains)

Domain ID domain_id	3dmtA01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	720 — NAD(P)-binding Rossmann-like Domain

Domain ID domain_id	3dmtA02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	360 — Dihydrodipicolinate Reductase; domain 2
Homologous superfamily homologous superfamily	10 — Dihydrodipicolinate Reductase; domain 2

Domain ID domain_id	3dmtB01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	720 — NAD(P)-binding Rossmann-like Domain

Domain ID domain_id	3dmtB02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	360 — Dihydrodipicolinate Reductase; domain 2
Homologous superfamily homologous superfamily	10 — Dihydrodipicolinate Reductase; domain 2

Domain ID domain_id	3dmtC01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	720 — NAD(P)-binding Rossmann-like Domain

Domain ID domain_id	3dmtC02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	360 — Dihydrodipicolinate Reductase; domain 2
Homologous superfamily homologous superfamily	10 — Dihydrodipicolinate Reductase; domain 2

Domain ID domain_id	3dmtD01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	720 — NAD(P)-binding Rossmann-like Domain

Domain ID domain_id	3dmtD02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	360 — Dihydrodipicolinate Reductase; domain 2
Homologous superfamily homologous superfamily	10 — Dihydrodipicolinate Reductase; domain 2

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Unit-cell length a length_a	78.755 Å
Unit-cell length b length_b	83.713 Å
Unit-cell length c length_c	105.611 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	96.44 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	6

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

Resolution resolution	2.300 Å
Low-resolution limit resolution_low	38.100 Å
R factor r_factor	0.1896
R_work r_work	0.1862
R_free r_free	0.2517

Structure of Glycosomal Glyceraldehyde-3-Phosphate Dehydrogenase from Trypanosoma cruzi in complex with the irreversible iodoacetate inhibitor

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

Glyceraldehyde-3-phosphate dehydrogenase, glycosomal

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

3dmt__assembly_1__model_1

3dmt__assembly_1__model_1 | I(q)

3dmt__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 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

CATH v4.4 (8 domains)

7. Citations (1)

Structure of Glycosomal Glyceraldehyde-3-Phosphate Dehydrogenase from Trypanosoma cruzi in complex with the irreversible iodoacetate inhibitor

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

Glyceraldehyde-3-phosphate dehydrogenase, glycosomal

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

3dmt__assembly_1__model_1

3dmt__assembly_1__model_1 | I(q)

3dmt__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 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

CATH v4.4 (8 domains)

7. Citations (1)