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1psd

THE ALLOSTERIC LIGAND SITE IN THE VMAX-TYPE COOPERATIVE ENZYME PHOSPHOGLYCERATE DEHYDROGENASE

Method: X-RAY DIFFRACTION
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1. Protein Identity and Related Structures Protein Identity & Related Structures

D-3-PHOSPHOGLYCERATE DEHYDROGENASE (PHOSPHOGLYCERATE DEHYDROGENASE)

Escherichia coli

UniProt P0A9T0

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 SERINE × 4 water × 4 Consistent with protein count

Other States of the Same Protein in the Database

Monomer

None

Homodimer

None

Homotetramer
1psd 1sc6 2p9c 2p9e 2p9g 2pa3

6 assemblies

Other homooligomers

None

Heteromeric or nucleic-acid complex

None

View Construct and Data Evidence
UniProt name SERA_ECOLI
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–409； UniProt 1–409 Author chain B； PDBConstruct 1–409； UniProt 1–409

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_id1psd
Deposition date deposition_date1995-05-02
Structure title titleTHE ALLOSTERIC LIGAND SITE IN THE VMAX-TYPE COOPERATIVE ENZYME PHOSPHOGLYCERATE DEHYDROGENASE
Keywords keywordsOXIDOREDUCTASE (NAD(A)); OXIDOREDUCTASE (NAD(A))
Experimental Method methodX-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.

1psd__assembly_1__model_1

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

Download this curve (.dat)

1psd__assembly_1__model_1 | I(q)

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

1psd__assembly_1__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）41.79 Å
Rg (electron density)41.33 Å
Total Rg41.60 Å
Atom count12456
Residues1616
Excluded volume222060 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 1psd__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 (4)

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6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

Domain ID domain_idd1psda1
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.2.1.4 — Formate/glycerate dehydrogenases, NAD-domain
Domain ID domain_idd1psda2
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.23 — Flavodoxin-like
Superfamily Superfamily superfamilyc.23.12 — Formate/glycerate dehydrogenase catalytic domain-like
Family Family familyc.23.12.1 — Formate/glycerate dehydrogenases, substrate-binding domain
Domain ID domain_idd1psda3
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.58 — Ferredoxin-like
Superfamily Superfamily superfamilyd.58.18 — ACT-like
Family Family familyd.58.18.1 — Phosphoglycerate dehydrogenase, regulatory (C-terminal) domain
Domain ID domain_idd1psdb1
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.2.1.4 — Formate/glycerate dehydrogenases, NAD-domain
Domain ID domain_idd1psdb2
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.23 — Flavodoxin-like
Superfamily Superfamily superfamilyc.23.12 — Formate/glycerate dehydrogenase catalytic domain-like
Family Family familyc.23.12.1 — Formate/glycerate dehydrogenases, substrate-binding domain
Domain ID domain_idd1psdb3
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.58 — Ferredoxin-like
Superfamily Superfamily superfamilyd.58.18 — ACT-like
Family Family familyd.58.18.1 — Phosphoglycerate dehydrogenase, regulatory (C-terminal) domain

CATH v4.4 (6 domains)

Domain ID domain_id1psdA01
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_id1psdA02
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_id1psdA03
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily260 — ACT domain
Domain ID domain_id1psdB01
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_id1psdB02
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_id1psdB03
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily260 — ACT domain
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7. Citations (3)