← Back to search
2pkq

Crystal structure of the photosynthetic A2B2-glyceraldehyde-3-phosphate dehydrogenase, complexed with NADP

Method: X-RAY DIFFRACTION
▼

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

Glyceraldehyde-3-phosphate dehydrogenase B

OrganismNot specified

UniProt P12860

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 4 Glyceraldehyde-3-phosphate dehydrogenase A × 2 （P19866） SULFATE ION × 9 NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 4 Consistent with protein count
2 Protein heterocomplex Heteromer Protein 4 Glyceraldehyde-3-phosphate dehydrogenase A × 2 （P19866） SULFATE ION × 12 NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 4 Consistent with protein count

Other States of the Same Protein in the Database

Monomer

None

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
2pkq 2pkq 7q53 7q54 7q55 7q56 7q57 9i06 9i07 9i3s

10 assemblies

View Construct and Data Evidence
UniProt name G3PB_SPIOL
Isoform —
PDB entities 1
Chains and sequence ranges Author chain O； PDBConstruct 1–368； UniProt 84–451 Author chain Q； PDBConstruct 1–368； UniProt 84–451 Author chain T； PDBConstruct 1–368； UniProt 84–451

Glyceraldehyde-3-phosphate dehydrogenase A

OrganismNot specified

UniProt P19866

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 4 Glyceraldehyde-3-phosphate dehydrogenase B × 2 （P12860） SULFATE ION × 9 NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 4 Consistent with protein count
2 Protein heterocomplex Heteromer Protein 4 Glyceraldehyde-3-phosphate dehydrogenase B × 2 （P12860） SULFATE ION × 12 NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 4 Consistent with protein count

Other States of the Same Protein in the Database

Monomer

None

Homodimer

None

Homotetramer
1jn0 1jn0 1nbo 1nbo 1rm3 1rm3 1rm4 1rm4 1rm5 1rm5 2hki 2pkr

14 assemblies; showing the first 12

Other homooligomers

None

Heteromeric or nucleic-acid complex
2pkq 2pkq 7q53 7q54 7q55 7q56 7q57 9i06 9i07 9i3s

10 assemblies

View Construct and Data Evidence
UniProt name G3PA_SPIOL
Isoform —
PDB entities 2
Chains and sequence ranges Author chain P； PDBConstruct 1–336； UniProt 66–401 Author chain R； PDBConstruct 1–336； UniProt 66–401 Author chain S； PDBConstruct 1–336； UniProt 66–401

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id2pkq
Deposition date deposition_date2007-04-18
Structure title titleCrystal structure of the photosynthetic A2B2-glyceraldehyde-3-phosphate dehydrogenase, complexed with NADP
Keywords keywordsRossmann fold, protein-NADP complex, OXIDOREDUCTASE; OXIDOREDUCTASE
Experimental Method methodX-RAY DIFFRACTION
▼

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.

2pkq__assembly_2__model_1

Assembly 2 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

2pkq__assembly_2__model_1 | I(q)

10-2 10-1 106 107 108 q (1/Angstrom) I(q)
100 plotted points; both axes use logarithmic scales.

2pkq__assembly_2__model_1 | P(r) · Pending

The new assembly/model P(r) has not been calculated yet This placeholder does not display legacy data r (Angstrom) P(r)
P(r) will be calculated and displayed separately for the same assembly/model.
Rg（Guinier）32.41 Å
Rg (electron density)31.87 Å
Total Rg32.46 Å
Atom count10578
Residues1370
Excluded volume188240 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 2pkq__assembly_1__model_1 tetrameric （4） Success 4.1.3-1-20251215 (887e7ef) View Download
2 1 2pkq__assembly_2__model_1 tetrameric （4） Success 4.1.3-1-20251215 (887e7ef) View Download
▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (4)

▼

6. Fold Classification (SCOP + CATH) 26 domains

SCOP 2.08 (14 domains)

Domain ID domain_idd2pkqo1
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.2 — NAD(P)-binding Rossmann-fold domains
Superfamily Superfamily superfamilyc.2.1 — NAD(P)-binding Rossmann-fold domains
Family Family familyc.2.1.3 — Glyceraldehyde-3-phosphate dehydrogenase-like, N-terminal domain
Domain ID domain_idd2pkqo2
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.81 — FwdE/GAPDH domain-like
Superfamily Superfamily superfamilyd.81.1 — Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain
Family Family familyd.81.1.1 — GAPDH-like
Domain ID domain_idd2pkqp1
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.2 — NAD(P)-binding Rossmann-fold domains
Superfamily Superfamily superfamilyc.2.1 — NAD(P)-binding Rossmann-fold domains
Family Family familyc.2.1.3 — Glyceraldehyde-3-phosphate dehydrogenase-like, N-terminal domain
Domain ID domain_idd2pkqp2
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.81 — FwdE/GAPDH domain-like
Superfamily Superfamily superfamilyd.81.1 — Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain
Family Family familyd.81.1.1 — GAPDH-like
Domain ID domain_idd2pkqp3
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd2pkqq1
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.2 — NAD(P)-binding Rossmann-fold domains
Superfamily Superfamily superfamilyc.2.1 — NAD(P)-binding Rossmann-fold domains
Family Family familyc.2.1.3 — Glyceraldehyde-3-phosphate dehydrogenase-like, N-terminal domain
Domain ID domain_idd2pkqq2
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.81 — FwdE/GAPDH domain-like
Superfamily Superfamily superfamilyd.81.1 — Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain
Family Family familyd.81.1.1 — GAPDH-like
Domain ID domain_idd2pkqr1
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.2 — NAD(P)-binding Rossmann-fold domains
Superfamily Superfamily superfamilyc.2.1 — NAD(P)-binding Rossmann-fold domains
Family Family familyc.2.1.3 — Glyceraldehyde-3-phosphate dehydrogenase-like, N-terminal domain
Domain ID domain_idd2pkqr2
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.81 — FwdE/GAPDH domain-like
Superfamily Superfamily superfamilyd.81.1 — Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain
Family Family familyd.81.1.1 — GAPDH-like
Domain ID domain_idd2pkqr3
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd2pkqs1
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.2 — NAD(P)-binding Rossmann-fold domains
Superfamily Superfamily superfamilyc.2.1 — NAD(P)-binding Rossmann-fold domains
Family Family familyc.2.1.3 — Glyceraldehyde-3-phosphate dehydrogenase-like, N-terminal domain
Domain ID domain_idd2pkqs2
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.81 — FwdE/GAPDH domain-like
Superfamily Superfamily superfamilyd.81.1 — Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain
Family Family familyd.81.1.1 — GAPDH-like
Domain ID domain_idd2pkqt1
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.2 — NAD(P)-binding Rossmann-fold domains
Superfamily Superfamily superfamilyc.2.1 — NAD(P)-binding Rossmann-fold domains
Family Family familyc.2.1.3 — Glyceraldehyde-3-phosphate dehydrogenase-like, N-terminal domain
Domain ID domain_idd2pkqt2
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.81 — FwdE/GAPDH domain-like
Superfamily Superfamily superfamilyd.81.1 — Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain
Family Family familyd.81.1.1 — GAPDH-like

CATH v4.4 (12 domains)

Domain ID domain_id2pkqO01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily720 — NAD(P)-binding Rossmann-like Domain
Domain ID domain_id2pkqO02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology360 — Dihydrodipicolinate Reductase; domain 2
Homologous superfamily homologous superfamily10 — Dihydrodipicolinate Reductase; domain 2
Domain ID domain_id2pkqP01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily720 — NAD(P)-binding Rossmann-like Domain
Domain ID domain_id2pkqP02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology360 — Dihydrodipicolinate Reductase; domain 2
Homologous superfamily homologous superfamily10 — Dihydrodipicolinate Reductase; domain 2
Domain ID domain_id2pkqQ01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily720 — NAD(P)-binding Rossmann-like Domain
Domain ID domain_id2pkqQ02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology360 — Dihydrodipicolinate Reductase; domain 2
Homologous superfamily homologous superfamily10 — Dihydrodipicolinate Reductase; domain 2
Domain ID domain_id2pkqR01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily720 — NAD(P)-binding Rossmann-like Domain
Domain ID domain_id2pkqR02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology360 — Dihydrodipicolinate Reductase; domain 2
Homologous superfamily homologous superfamily10 — Dihydrodipicolinate Reductase; domain 2
Domain ID domain_id2pkqS01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily720 — NAD(P)-binding Rossmann-like Domain
Domain ID domain_id2pkqS02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology360 — Dihydrodipicolinate Reductase; domain 2
Homologous superfamily homologous superfamily10 — Dihydrodipicolinate Reductase; domain 2
Domain ID domain_id2pkqT01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily720 — NAD(P)-binding Rossmann-like Domain
Domain ID domain_id2pkqT02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology360 — Dihydrodipicolinate Reductase; domain 2
Homologous superfamily homologous superfamily10 — Dihydrodipicolinate Reductase; domain 2
▶

7. Citations (4)