4gpd

THE STRUCTURE OF LOBSTER APO-D-GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE AT 3.0 ANGSTROMS RESOLUTION

Method: X-RAY DIFFRACTION

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

APO-D-GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE

Homarus americanus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 4	water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	G3P_HOMAM
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain 1； PDBConstruct 1–333； UniProt 1–333 Author chain 2； PDBConstruct 1–333； UniProt 1–333 Author chain 3； PDBConstruct 1–333； UniProt 1–333 Author chain 4； PDBConstruct 1–333； UniProt 1–333

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	4gpd
Deposition date deposition_date	1988-01-04
Structure title title	THE STRUCTURE OF LOBSTER APO-D-GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE AT 3.0 ANGSTROMS RESOLUTION
Keywords keywords	OXIDOREDUCTASE(ALDEHYDE(D)-NAD(A)); OXIDOREDUCTASE(ALDEHYDE(D)-NAD(A))
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.

4gpd__assembly_1__model_1

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

Download this curve (.dat)

4gpd__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4gpd__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	32.99 Å
Rg (electron density)	32.21 Å
Total Rg	32.94 Å
Atom count	10028
Residues	1332
Excluded volume	179730 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4gpd__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 (2)

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6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

Domain ID domain_id	d4gpd11
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	d4gpd12
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	d4gpd21
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	d4gpd22
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	d4gpd31
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	d4gpd32
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	d4gpd41
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	d4gpd42
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	4gpd101
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	4gpd102
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	4gpd201
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	4gpd202
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	4gpd301
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	4gpd302
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	4gpd401
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	4gpd402
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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7. Citations (10)

Structure of lobster apo-D-glyceraldehyde-3-phosphate dehydrogenase at 3.0 A resolution.

J.Mol.Biol. (1980)

PMID: 7411626 · DOI: 10.1016/0022-2836(80)90069-8 PRIMARY

Anion Binding Sites in the Active Center of D-Glyceraldehyde-3-Phosphate Dehydrogenase

J.Mol.Biol. (1976)

Studies on Coenzyme Binding to Glyceraldehyde-3-Phosphate Dehydrogenase

J.Mol.Biol. (1976)

Studies of Asymmetry in the Three-Dimensional Structure of Lobster D-Glyceraldehyde-3-Phosphate Dehydrogenase

J.Biol.Chem. (1975)

A Comparison of the Binding and Function of Nad with Respect to Lactate Dehydrogenase and Glyceraldehyde-3-Phosphate Dehydrogenase

;STRUCTURE AND CONFORMATION OF NUCLEIC ACIDS AND PROTEIN-NUCLEIC ACID INTERACTIONS : PROCEEDINGS OF THE FOURTH ANNUAL HARRY STEENBOCK SYMPOSIUM, JUNE 16-19, 1974, MADISON, WISCONSIN ; (1975)

Sequence Variability and Structure of D-Glyceraldehyde-3-Phosphate Dehydrogenase

J.Biol.Chem. (1975)

An Application of the Molecular Replacement Technique in Direct Space to a Known Protein Structure

Acta Crystallogr.,Sect.A (1975)

Three-Dimensional Structure of D-Glyceraldehyde-3-Phosphate Dehydrogenase

J.Mol.Biol. (1974)

Structure Determination of Crystalline Lobster D-Glyceraldehyde-3-Phosphate Dehydrogenase

J.Mol.Biol. (1974)

D-Glyceraldehyde-3-Phosphate Dehydrogenase, Three-Dimensional Structure and Evolutionary Significance

Proc.Natl.Acad.Sci.USA (1973)

Unit-cell length a length_a	83.019 Å
Unit-cell length b length_b	80.956 Å
Unit-cell length c length_c	82.545 Å
Unit-cell angle α angle_alpha	110.85 °
Unit-cell angle β angle_beta	71.47 °
Unit-cell angle γ angle_gamma	116.86 °
Molecules per unit cell Z z_pdb	4

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

Resolution resolution	2.800 Å
Low-resolution limit resolution_low	6.000 Å
R factor r_factor	0.2180
R_work r_work	—
R_free r_free	—

Description description	APO-D-GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE
Molecular weight formula_weight	35757.9 kDa
EC 编号 ec_number	1.2.1.12
Source method src_method	man
Copy count entity_count	4

Polymer type type	polypeptide(L)
Chain IDs strand_id	1,2,3,4
Atom count atom_count	10150

THE STRUCTURE OF LOBSTER APO-D-GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE AT 3.0 ANGSTROMS RESOLUTION

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

APO-D-GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE

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

4gpd__assembly_1__model_1

4gpd__assembly_1__model_1 | I(q)

4gpd__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

5. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 water

6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

CATH v4.4 (8 domains)

7. Citations (10)

Source organism organism	Homarus americanus
Common name common_name	American lobster
NCBI taxonomy ID ncbi_taxonomy_id	6706

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	122

THE STRUCTURE OF LOBSTER APO-D-GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE AT 3.0 ANGSTROMS RESOLUTION

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

APO-D-GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE

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

4gpd__assembly_1__model_1

4gpd__assembly_1__model_1 | I(q)

4gpd__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

5. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 water

6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

CATH v4.4 (8 domains)

7. Citations (10)