3gnq

Crystal structure of glyceraldehyde-3-phosphate dehydrogenase, type I from Burkholderia pseudomallei

Method: X-RAY DIFFRACTION

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

Glyceraldehyde-3-phosphate dehydrogenase, type I

Burkholderia pseudomallei

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 × 3 water × 4	Consistent with protein count
10	Protein homooligomer	Homooligomer	Protein 2	NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 2 water × 2	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 1 water × 2	Consistent with protein count
3	Protein homooligomer	Homooligomer	Protein 2	NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 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 water × 2	Consistent with protein count
6	Protein homooligomer	Homooligomer	Protein 4	NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 4 water × 4	Consistent with protein count
7	Protein homooligomer	Homooligomer	Protein 2	NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 2 water × 2	Consistent with protein count
8	Protein homooligomer	Homooligomer	Protein 2	NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 2 water × 2	Consistent with protein count
9	Protein homooligomer	Homooligomer	Protein 2	NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q3JNL6_BURP1
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 9–344； UniProt 1–336 Author chain B； PDBConstruct 9–344； UniProt 1–336 Author chain C； PDBConstruct 9–344； UniProt 1–336 Author chain D； PDBConstruct 9–344； UniProt 1–336 Author chain E； PDBConstruct 9–344； UniProt 1–336 Author chain F； PDBConstruct 9–344； UniProt 1–336 Author chain G； PDBConstruct 9–344； UniProt 1–336 Author chain H； PDBConstruct 9–344； UniProt 1–336

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	3gnq
Deposition date deposition_date	2009-03-17
Structure title title	Crystal structure of glyceraldehyde-3-phosphate dehydrogenase, type I from Burkholderia pseudomallei
Keywords keywords	;deCODE biostructures, SSGCID, UWPPG, SBRI, NIAID, Oxidoreductase, Structural Genomics, Seattle Structural Genomics Center for Infectious Disease ;; 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.

3gnq__assembly_1__model_1

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

Download this curve (.dat)

3gnq__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3gnq__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	32.53 Å
Rg (electron density)	31.82 Å
Total Rg	32.54 Å
Atom count	10197
Residues	1339
Excluded volume	180400 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3gnq__assembly_1__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3gnq__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`3gnq__assembly_3__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`3gnq__assembly_4__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
5	1	`3gnq__assembly_5__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
6	1	`3gnq__assembly_6__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
7	1	`3gnq__assembly_7__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
8	1	`3gnq__assembly_8__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
9	1	`3gnq__assembly_9__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
10	1	`3gnq__assembly_10__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 (3)

Entity 1 Entity 1 polymer

Description description	Glyceraldehyde-3-phosphate dehydrogenase, type I
Molecular weight formula_weight	37194.1 kDa
EC 编号 ec_number	1.2.1.-
Source method src_method	man
Copy count entity_count	8

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G,H
Atom count atom_count	21007

MAHHHHHHMTIRVAINGYGRIGRNTLRAFYENGKKHDLEIVAINDLGDAKTNAHLTQYDTAHGKFPGEVSVDGDYLVVNGDRIRVLANRNPAELPWGELGVDVVMECTGFFTSKEKASAHLKGGAKKVIISAPGGKDVDATIVYGVNHDVLKAEHTVISNASCTTNCLAPLVKPLNDKIGLETGLMTTIHAYTNDQVLTDVYHEDLRRARSATHSQIPTKTGAAAAVGLVLPELNGKLDGYAIRVPTINVSIVDLSFIAKRDTTAAEVNAIMKEASEGALKGILGYNEAPLVSIDFNHNPASSTFDATLTKVSGRLVKVSSWYDNEWGFSNRMLDTAIALANAK

Source Source

Source organism organism	Burkholderia pseudomallei
NCBI taxonomy ID ncbi_taxonomy_id	320372
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	NICOTINAMIDE-ADENINE-DINUCLEOTIDE
Molecular weight formula_weight	663.4 kDa
Source method src_method	syn
Copy count entity_count	7

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	538

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6. Fold Classification (SCOP + CATH) 16 domains

CATH v4.4 (16 domains)

Domain ID domain_id	3gnqA01
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	3gnqA02
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	3gnqB01
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	3gnqB02
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	3gnqC01
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	3gnqC02
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	3gnqD01
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	3gnqD02
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	3gnqE01
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	3gnqE02
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	3gnqF01
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	3gnqF02
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	3gnqG01
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	3gnqG02
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	3gnqH01
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	3gnqH02
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	90.932 Å
Unit-cell length b length_b	173.797 Å
Unit-cell length c length_c	93.501 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	93.29 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	16

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

Resolution resolution	2.400 Å
Low-resolution limit resolution_low	48.840 Å
R factor r_factor	0.2070
R_work r_work	0.2040
R_free r_free	0.2630

Crystal structure of glyceraldehyde-3-phosphate dehydrogenase, type I from Burkholderia pseudomallei

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

Glyceraldehyde-3-phosphate dehydrogenase, type I

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

3gnq__assembly_1__model_1

3gnq__assembly_1__model_1 | I(q)

3gnq__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 16 domains

CATH v4.4 (16 domains)

7. Citations (1)

Crystal structure of glyceraldehyde-3-phosphate dehydrogenase, type I from Burkholderia pseudomallei

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

Glyceraldehyde-3-phosphate dehydrogenase, type I

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

3gnq__assembly_1__model_1

3gnq__assembly_1__model_1 | I(q)

3gnq__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 16 domains

CATH v4.4 (16 domains)

7. Citations (1)