3rvd

Crystal structure of the binary complex, obtained by soaking, of photosyntetic a4 glyceraldehyde 3-phosphate dehydrogenase (gapdh) with cp12-2, both from arabidopsis thaliana.

Method: X-RAY DIFFRACTION

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

Glyceraldehyde-3-phosphate dehydrogenase A, chloroplastic

Arabidopsis thaliana

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 6	Photosyntetic glyceraldehyde-3-phosphate dehydrogenase (a4 isoform) × 2 （Q9LZP9） NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 4 SULFATE ION × 15 water × 6	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 6	Photosyntetic glyceraldehyde-3-phosphate dehydrogenase (a4 isoform) × 2 （Q9LZP9） NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 4 SULFATE ION × 7 water × 6	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 6	Photosyntetic glyceraldehyde-3-phosphate dehydrogenase (a4 isoform) × 2 （Q9LZP9） NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 4 SULFATE ION × 12 water × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	G3PA_ARATH
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–337； UniProt 61–396 Author chain B； PDBConstruct 2–337； UniProt 61–396 Author chain C； PDBConstruct 2–337； UniProt 61–396 Author chain D； PDBConstruct 2–337； UniProt 61–396 Author chain E； PDBConstruct 2–337； UniProt 61–396 Author chain F； PDBConstruct 2–337； UniProt 61–396 Author chain G； PDBConstruct 2–337； UniProt 61–396 Author chain H； PDBConstruct 2–337； UniProt 61–396 Author chain O； PDBConstruct 2–337； UniProt 61–396 Author chain Q； PDBConstruct 2–337； UniProt 61–396

Photosyntetic glyceraldehyde-3-phosphate dehydrogenase (a4 isoform)

Arabidopsis thaliana

UniProt Q9LZP9

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 6	Glyceraldehyde-3-phosphate dehydrogenase A, chloroplastic × 4 （P25856） NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 4 SULFATE ION × 15 water × 6	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 6	Glyceraldehyde-3-phosphate dehydrogenase A, chloroplastic × 4 （P25856） NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 4 SULFATE ION × 7 water × 6	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 6	Glyceraldehyde-3-phosphate dehydrogenase A, chloroplastic × 4 （P25856） NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 4 SULFATE ION × 12 water × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q9LZP9_ARATH
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain I； PDBConstruct 5–82； UniProt 54–131 Author chain J； PDBConstruct 5–82； UniProt 54–131 Author chain K； PDBConstruct 5–82； UniProt 54–131 Author chain L； PDBConstruct 5–82； UniProt 54–131 Author chain M； PDBConstruct 5–82； UniProt 54–131 Author chain N； PDBConstruct 5–82； UniProt 54–131

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	3rvd
Deposition date deposition_date	2011-05-06
Structure title title	Crystal structure of the binary complex, obtained by soaking, of photosyntetic a4 glyceraldehyde 3-phosphate dehydrogenase (gapdh) with cp12-2, both from arabidopsis thaliana.
Keywords keywords	Rossmann fold, Calvin cycle, binary complex, chloroplast, OXIDOREDUCTASE-PROTEIN BINDING complex; OXIDOREDUCTASE/PROTEIN BINDING
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.

3rvd__assembly_1__model_1

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

Download this curve (.dat)

3rvd__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3rvd__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	32.40 Å
Rg (electron density)	31.74 Å
Total Rg	32.42 Å
Atom count	10817
Residues	1387
Excluded volume	191950 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3rvd__assembly_1__model_1`	hexameric （6）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3rvd__assembly_2__model_1`	hexameric （6）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`3rvd__assembly_3__model_1`	hexameric （6）	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 A, chloroplastic
Molecular weight formula_weight	36391.6 kDa
EC 编号 ec_number	1.2.1.13
Source method src_method	man
Copy count entity_count	10

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G,H,O,Q
Atom count atom_count	27674

AKLKVAINGFGRIGRNFLRCWHGRKDSPLDIIAINDTGGVKQASHLLKYDSTLGIFDADVKPSGETAISVDGKIIQVVSNRNPSLLPWKELGIDIVIEGTGVFVDREGAGKHIEAGAKKVIITAPGKGDIPTYVVGVNADAYSHDEPIISNASCTTNCLAPFVKVLDQKFGIIKGTMTTTHSYTGDQRLLDASHRDLRRARAAALNIVPTSTGAAKAVALVLPNLKGKLNGIALRVPTPNVSVVDLVVQVSKKTFAEEVNAAFRDSAEKELKGILDVCDEPLVSVDFRCSDFSTTIDSSLTMVMGDDMVKVIAWYDNEWGYSQRVVDLADIVANNWK

Source Source

Source organism organism	Arabidopsis thaliana
Common name common_name	mouse-ear cress,thale-cress
NCBI taxonomy ID ncbi_taxonomy_id	3702
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Photosyntetic glyceraldehyde-3-phosphate dehydrogenase (a4 isoform)
Molecular weight formula_weight	8754.4 kDa
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	I,J,K,L,M,N

GSHMAAPEGGISDVVEKSIKEAQETCAGDPVSGECVAAWDEVEELSAAASHARDKKKADGSDPLEEYCKDNPETNECRTYDN

Source Source

Source organism organism	Arabidopsis thaliana
Common name common_name	mouse-ear cress,thale-cress
NCBI taxonomy ID ncbi_taxonomy_id	3702
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	10

Entity 4 Entity 4 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	28

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	556

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6. Fold Classification (SCOP + CATH) 20 domains

CATH v4.4 (20 domains)

Domain ID domain_id	3rvdA01
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	3rvdA02
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	3rvdB01
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	3rvdB02
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	3rvdC01
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	3rvdC02
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	3rvdD01
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	3rvdD02
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	3rvdE01
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	3rvdE02
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	3rvdF01
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	3rvdF02
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	3rvdG01
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	3rvdG02
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	3rvdH01
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	3rvdH02
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	3rvdO01
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	3rvdO02
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	3rvdQ01
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	3rvdQ02
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	153.183 Å
Unit-cell length b length_b	188.750 Å
Unit-cell length c length_c	312.170 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	80

Space group space_group	I 2 2 2
Space-group number int_tables_number	23
Crystal system crystal_system	—

Resolution resolution	2.700 Å
Low-resolution limit resolution_low	94.610 Å
R factor r_factor	0.2470
R_work r_work	0.2470
R_free r_free	0.3180

Crystal structure of the binary complex, obtained by soaking, of photosyntetic a4 glyceraldehyde 3-phosphate dehydrogenase (gapdh) with cp12-2, both from arabidopsis thaliana.

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

Glyceraldehyde-3-phosphate dehydrogenase A, chloroplastic

State in the Current Structure

Other States of the Same Protein in the Database

Photosyntetic glyceraldehyde-3-phosphate dehydrogenase (a4 isoform)

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

3rvd__assembly_1__model_1

3rvd__assembly_1__model_1 | I(q)

3rvd__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) 20 domains

CATH v4.4 (20 domains)

7. Citations (2)

Crystal structure of the binary complex, obtained by soaking, of photosyntetic a4 glyceraldehyde 3-phosphate dehydrogenase (gapdh) with cp12-2, both from arabidopsis thaliana.

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

Glyceraldehyde-3-phosphate dehydrogenase A, chloroplastic

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Photosyntetic glyceraldehyde-3-phosphate dehydrogenase (a4 isoform)

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

3rvd__assembly_1__model_1

3rvd__assembly_1__model_1 | I(q)

3rvd__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) 20 domains

CATH v4.4 (20 domains)

7. Citations (2)