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1pby

Structure of the Phenylhydrazine Adduct of the Quinohemoprotein Amine Dehydrogenase from Paracoccus denitrificans at 1.7 A Resolution

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

quinohemoprotein amine dehydrogenase 60 kDa subunit

Paracoccus denitrificans

UniProt Q8VUT0

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 3 quinohemoprotein amine dehydrogenase 40 kDa subunit × 1 quinohemoprotein amine dehydrogenase 9 kDa subunit × 1 HEME C × 2 TERTIARY-BUTYL ALCOHOL × 4 water × 3 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
1jju 1pby

2 assemblies

View Construct and Data Evidence
UniProt name Q8VUT0_PARDE
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–489； UniProt 24–512

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_id1pby
Deposition date deposition_date2003-05-15
Structure title titleStructure of the Phenylhydrazine Adduct of the Quinohemoprotein Amine Dehydrogenase from Paracoccus denitrificans at 1.7 A Resolution
Keywords keywordsQUINOHEMOPROTEIN, AMINE DEHYDROGENASE, OXIDOREDUCTASE; OXIDOREDUCTASE
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.

1pby__assembly_1__model_1

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

Download this curve (.dat)

1pby__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.

1pby__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）31.05 Å
Rg (electron density)30.45 Å
Total Rg31.10 Å
Atom count7037
Residues904
Excluded volume124310 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 1pby__assembly_1__model_1 trimeric （3） 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 (6)

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6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (7 domains)

Domain ID domain_idd1pbya1
Class classa — All alpha proteins
Fold Fold folda.3 — Cytochrome c
Superfamily Superfamily superfamilya.3.1 — Cytochrome c
Family Family familya.3.1.7 — Quinohemoprotein amine dehydrogenase A chain, domains 1 and 2
Domain ID domain_idd1pbya2
Class classa — All alpha proteins
Fold Fold folda.3 — Cytochrome c
Superfamily Superfamily superfamilya.3.1 — Cytochrome c
Family Family familya.3.1.7 — Quinohemoprotein amine dehydrogenase A chain, domains 1 and 2
Domain ID domain_idd1pbya3
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.18 — E set domains
Family Family familyb.1.18.14 — Quinohemoprotein amine dehydrogenase A chain, domains 4 and 5
Domain ID domain_idd1pbya4
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.18 — E set domains
Family Family familyb.1.18.14 — Quinohemoprotein amine dehydrogenase A chain, domains 4 and 5
Domain ID domain_idd1pbya5
Class classb — All beta proteins
Fold Fold foldb.61 — Streptavidin-like
Superfamily Superfamily superfamilyb.61.4 — Quinohemoprotein amine dehydrogenase A chain, domain 3
Family Family familyb.61.4.1 — Quinohemoprotein amine dehydrogenase A chain, domain 3
Domain ID domain_idd1pbyb_
Class classb — All beta proteins
Fold Fold foldb.69 — 7-bladed beta-propeller
Superfamily Superfamily superfamilyb.69.2 — YVTN repeat-like/Quinoprotein amine dehydrogenase
Family Family familyb.69.2.2 — Quinohemoprotein amine dehydrogenase B chain
Domain ID domain_idd1pbyc_
Class classa — All alpha proteins
Fold Fold folda.137 — Non-globular all-alpha subunits of globular proteins
Superfamily Superfamily superfamilya.137.9 — Quinohemoprotein amine dehydrogenase C chain
Family Family familya.137.9.1 — Quinohemoprotein amine dehydrogenase C chain

CATH v4.4 (5 domains)

Domain ID domain_id1pbyA02
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology128 — Lipocalin
Homologous superfamily homologous superfamily120 — Quinohemoprotein amine dehydrogenase alpha subunit, domain 2
Domain ID domain_id1pbyA03
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id1pbyA04
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id1pbyB00
Class class2 — Mainly Beta
Architecture architecture130 — 7 Propeller
Topology topology10 — Methylamine Dehydrogenase; Chain H
Homologous superfamily homologous superfamily10 — YVTN repeat-like/Quinoprotein amine dehydrogenase
Domain ID domain_id1pbyC00
Class class4 — Few Secondary Structures
Architecture architecture10 — Irregular
Topology topology940 — Quinohemoprotein amine dehydrogenase
Homologous superfamily homologous superfamily10 — Quinohemoprotein amine dehydrogenase, gamma subunit structural domain
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7. Citations (2)