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1zpd

PYRUVATE DECARBOXYLASE FROM ZYMOMONAS MOBILIS

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

PYRUVATE DECARBOXYLASE

Zymomonas mobilis

UniProt P06672

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein homooligomer Homooligomer Protein 4 MAGNESIUM ION × 4 MONO-{4-[(4-AMINO-2-METHYL-PYRIMIDIN-5-YLMETHYL)-AMINO]-2-HYDROXY-3-MERCAPTO-PENT-3-ENYL-PHOSPHONO} ESTER × 4 CITRIC ACID × 4 water × 4 Consistent with protein count

Other States of the Same Protein in the Database

Monomer

None

Homodimer
2wvg 2wvg 2wvg 2wvg

4 assemblies

Homotetramer
1zpd 2wva 2wva 2wvg 2wvh 2wvh 3oe1 4zp1 5tma

9 assemblies

Other homooligomers

None

Heteromeric or nucleic-acid complex

None

View Construct and Data Evidence
UniProt name PDC_ZYMMO
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–566； UniProt 1–566 Author chain B； PDBConstruct 1–566； UniProt 1–566 Author chain E； PDBConstruct 1–566； UniProt 1–566 Author chain F； PDBConstruct 1–566； UniProt 1–566

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_id1zpd
Deposition date deposition_date1998-04-17
Structure title titlePYRUVATE DECARBOXYLASE FROM ZYMOMONAS MOBILIS
Keywords keywordsALCOHOL FERMENTATION, THIAMIN DIPHOSPHATE, DECARBOXYLASE; ALCOHOL FERMENTATION
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.

1zpd__assembly_1__model_1

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

Download this curve (.dat)

1zpd__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.

1zpd__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）38.19 Å
Rg (electron density)37.45 Å
Total Rg38.04 Å
Atom count17220
Residues2260
Excluded volume306770 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 1zpd__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 (5)

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6. Fold Classification (SCOP + CATH) 24 domains

SCOP 2.08 (12 domains)

Domain ID domain_idd1zpda1
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.31 — DHS-like NAD/FAD-binding domain
Superfamily Superfamily superfamilyc.31.1 — DHS-like NAD/FAD-binding domain
Family Family familyc.31.1.3 — Pyruvate oxidase and decarboxylase, middle domain
Domain ID domain_idd1zpda2
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.36 — Thiamin diphosphate-binding fold (THDP-binding)
Superfamily Superfamily superfamilyc.36.1 — Thiamin diphosphate-binding fold (THDP-binding)
Family Family familyc.36.1.5 — Pyruvate oxidase and decarboxylase Pyr module
Domain ID domain_idd1zpda3
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.36 — Thiamin diphosphate-binding fold (THDP-binding)
Superfamily Superfamily superfamilyc.36.1 — Thiamin diphosphate-binding fold (THDP-binding)
Family Family familyc.36.1.9 — Pyruvate oxidase and decarboxylase PP module
Domain ID domain_idd1zpdb1
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.31 — DHS-like NAD/FAD-binding domain
Superfamily Superfamily superfamilyc.31.1 — DHS-like NAD/FAD-binding domain
Family Family familyc.31.1.3 — Pyruvate oxidase and decarboxylase, middle domain
Domain ID domain_idd1zpdb2
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.36 — Thiamin diphosphate-binding fold (THDP-binding)
Superfamily Superfamily superfamilyc.36.1 — Thiamin diphosphate-binding fold (THDP-binding)
Family Family familyc.36.1.5 — Pyruvate oxidase and decarboxylase Pyr module
Domain ID domain_idd1zpdb3
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.36 — Thiamin diphosphate-binding fold (THDP-binding)
Superfamily Superfamily superfamilyc.36.1 — Thiamin diphosphate-binding fold (THDP-binding)
Family Family familyc.36.1.9 — Pyruvate oxidase and decarboxylase PP module
Domain ID domain_idd1zpde1
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.31 — DHS-like NAD/FAD-binding domain
Superfamily Superfamily superfamilyc.31.1 — DHS-like NAD/FAD-binding domain
Family Family familyc.31.1.3 — Pyruvate oxidase and decarboxylase, middle domain
Domain ID domain_idd1zpde2
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.36 — Thiamin diphosphate-binding fold (THDP-binding)
Superfamily Superfamily superfamilyc.36.1 — Thiamin diphosphate-binding fold (THDP-binding)
Family Family familyc.36.1.5 — Pyruvate oxidase and decarboxylase Pyr module
Domain ID domain_idd1zpde3
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.36 — Thiamin diphosphate-binding fold (THDP-binding)
Superfamily Superfamily superfamilyc.36.1 — Thiamin diphosphate-binding fold (THDP-binding)
Family Family familyc.36.1.9 — Pyruvate oxidase and decarboxylase PP module
Domain ID domain_idd1zpdf1
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.31 — DHS-like NAD/FAD-binding domain
Superfamily Superfamily superfamilyc.31.1 — DHS-like NAD/FAD-binding domain
Family Family familyc.31.1.3 — Pyruvate oxidase and decarboxylase, middle domain
Domain ID domain_idd1zpdf2
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.36 — Thiamin diphosphate-binding fold (THDP-binding)
Superfamily Superfamily superfamilyc.36.1 — Thiamin diphosphate-binding fold (THDP-binding)
Family Family familyc.36.1.5 — Pyruvate oxidase and decarboxylase Pyr module
Domain ID domain_idd1zpdf3
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.36 — Thiamin diphosphate-binding fold (THDP-binding)
Superfamily Superfamily superfamilyc.36.1 — Thiamin diphosphate-binding fold (THDP-binding)
Family Family familyc.36.1.9 — Pyruvate oxidase and decarboxylase PP module

CATH v4.4 (12 domains)

Domain ID domain_id1zpdA01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily970 — Thiamin diphosphate (ThDP)-binding fold, Pyr/PP domains
Domain ID domain_id1zpdA02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily1220 — TPP-binding domain
Domain ID domain_id1zpdA03
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily970 — Thiamin diphosphate (ThDP)-binding fold, Pyr/PP domains
Domain ID domain_id1zpdB01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily970 — Thiamin diphosphate (ThDP)-binding fold, Pyr/PP domains
Domain ID domain_id1zpdB02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily1220 — TPP-binding domain
Domain ID domain_id1zpdB03
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily970 — Thiamin diphosphate (ThDP)-binding fold, Pyr/PP domains
Domain ID domain_id1zpdE01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily970 — Thiamin diphosphate (ThDP)-binding fold, Pyr/PP domains
Domain ID domain_id1zpdE02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily1220 — TPP-binding domain
Domain ID domain_id1zpdE03
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily970 — Thiamin diphosphate (ThDP)-binding fold, Pyr/PP domains
Domain ID domain_id1zpdF01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily970 — Thiamin diphosphate (ThDP)-binding fold, Pyr/PP domains
Domain ID domain_id1zpdF02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily1220 — TPP-binding domain
Domain ID domain_id1zpdF03
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily970 — Thiamin diphosphate (ThDP)-binding fold, Pyr/PP domains
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7. Citations (1)