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1ykp

Protocatechuate 3,4-Dioxygenase Y408H mutant bound to DHB

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

Protocatechuate 3,4-dioxygenase alpha chain

Pseudomonas putida

UniProt P00436

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 24 Protocatechuate 3,4-dioxygenase beta chain × 12 （P00437） 3,4-DIHYDROXYBENZOIC ACID × 12 FE (III) ION × 12 water × 24 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
1ykk 1ykl 1ykm 1ykn 1yko 1ykp 2pcd 3lkt 3lmx 3lxv 3mfl 3mi1

37 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name PCXA_PSEPU
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–200； UniProt 1–200 Author chain C； PDBConstruct 1–200； UniProt 1–200 Author chain E； PDBConstruct 1–200； UniProt 1–200 Author chain G； PDBConstruct 1–200； UniProt 1–200 Author chain I； PDBConstruct 1–200； UniProt 1–200 Author chain K； PDBConstruct 1–200； UniProt 1–200

Protocatechuate 3,4-dioxygenase beta chain

Pseudomonas putida

UniProt P00437

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 24 Protocatechuate 3,4-dioxygenase alpha chain × 12 （P00436） 3,4-DIHYDROXYBENZOIC ACID × 12 FE (III) ION × 12 water × 24 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
1ykk 1ykl 1ykm 1ykn 1yko 1ykp 2pcd 3lkt 3lmx 3lxv 3mfl 3mi1

37 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name PCXB_PSEPU
Isoform —
PDB entities 2
Chains and sequence ranges Author chain B； PDBConstruct 1–238； UniProt 1–238 Author chain D； PDBConstruct 1–238； UniProt 1–238 Author chain F； PDBConstruct 1–238； UniProt 1–238 Author chain H； PDBConstruct 1–238； UniProt 1–238 Author chain J； PDBConstruct 1–238； UniProt 1–238 Author chain L； PDBConstruct 1–238； UniProt 1–238

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_id1ykp
Deposition date deposition_date2005-01-18
Structure title titleProtocatechuate 3,4-Dioxygenase Y408H mutant bound to DHB
Keywords keywordsprotocatechuate, catechol, 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.

1ykp__assembly_1__model_1

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

Download this curve (.dat)

1ykp__assembly_1__model_1 | I(q)

10-2 10-1 106 107 108 109 q (1/Angstrom) I(q)
100 plotted points; both axes use logarithmic scales.

1ykp__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）54.22 Å
Rg (electron density)53.10 Å
Total Rg53.32 Å
Atom count41520
Residues5244
Excluded volume730260 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 1ykp__assembly_1__model_1 24-meric （24） 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_idd1ykpa_
Class classb — All beta proteins
Fold Fold foldb.3 — Prealbumin-like
Superfamily Superfamily superfamilyb.3.6 — Aromatic compound dioxygenase
Family Family familyb.3.6.1 — Aromatic compound dioxygenase
Domain ID domain_idd1ykpb_
Class classb — All beta proteins
Fold Fold foldb.3 — Prealbumin-like
Superfamily Superfamily superfamilyb.3.6 — Aromatic compound dioxygenase
Family Family familyb.3.6.1 — Aromatic compound dioxygenase
Domain ID domain_idd1ykpc_
Class classb — All beta proteins
Fold Fold foldb.3 — Prealbumin-like
Superfamily Superfamily superfamilyb.3.6 — Aromatic compound dioxygenase
Family Family familyb.3.6.1 — Aromatic compound dioxygenase
Domain ID domain_idd1ykpd_
Class classb — All beta proteins
Fold Fold foldb.3 — Prealbumin-like
Superfamily Superfamily superfamilyb.3.6 — Aromatic compound dioxygenase
Family Family familyb.3.6.1 — Aromatic compound dioxygenase
Domain ID domain_idd1ykpe_
Class classb — All beta proteins
Fold Fold foldb.3 — Prealbumin-like
Superfamily Superfamily superfamilyb.3.6 — Aromatic compound dioxygenase
Family Family familyb.3.6.1 — Aromatic compound dioxygenase
Domain ID domain_idd1ykpf_
Class classb — All beta proteins
Fold Fold foldb.3 — Prealbumin-like
Superfamily Superfamily superfamilyb.3.6 — Aromatic compound dioxygenase
Family Family familyb.3.6.1 — Aromatic compound dioxygenase
Domain ID domain_idd1ykpg_
Class classb — All beta proteins
Fold Fold foldb.3 — Prealbumin-like
Superfamily Superfamily superfamilyb.3.6 — Aromatic compound dioxygenase
Family Family familyb.3.6.1 — Aromatic compound dioxygenase
Domain ID domain_idd1ykph_
Class classb — All beta proteins
Fold Fold foldb.3 — Prealbumin-like
Superfamily Superfamily superfamilyb.3.6 — Aromatic compound dioxygenase
Family Family familyb.3.6.1 — Aromatic compound dioxygenase
Domain ID domain_idd1ykpi_
Class classb — All beta proteins
Fold Fold foldb.3 — Prealbumin-like
Superfamily Superfamily superfamilyb.3.6 — Aromatic compound dioxygenase
Family Family familyb.3.6.1 — Aromatic compound dioxygenase
Domain ID domain_idd1ykpj_
Class classb — All beta proteins
Fold Fold foldb.3 — Prealbumin-like
Superfamily Superfamily superfamilyb.3.6 — Aromatic compound dioxygenase
Family Family familyb.3.6.1 — Aromatic compound dioxygenase
Domain ID domain_idd1ykpk_
Class classb — All beta proteins
Fold Fold foldb.3 — Prealbumin-like
Superfamily Superfamily superfamilyb.3.6 — Aromatic compound dioxygenase
Family Family familyb.3.6.1 — Aromatic compound dioxygenase
Domain ID domain_idd1ykpl_
Class classb — All beta proteins
Fold Fold foldb.3 — Prealbumin-like
Superfamily Superfamily superfamilyb.3.6 — Aromatic compound dioxygenase
Family Family familyb.3.6.1 — Aromatic compound dioxygenase

CATH v4.4 (12 domains)

Domain ID domain_id1ykpA00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology130 — Protocatechuate 3,4-Dioxygenase, subunit A
Homologous superfamily homologous superfamily10 — Aromatic compound dioxygenase
Domain ID domain_id1ykpB00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology130 — Protocatechuate 3,4-Dioxygenase, subunit A
Homologous superfamily homologous superfamily10 — Aromatic compound dioxygenase
Domain ID domain_id1ykpC00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology130 — Protocatechuate 3,4-Dioxygenase, subunit A
Homologous superfamily homologous superfamily10 — Aromatic compound dioxygenase
Domain ID domain_id1ykpD00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology130 — Protocatechuate 3,4-Dioxygenase, subunit A
Homologous superfamily homologous superfamily10 — Aromatic compound dioxygenase
Domain ID domain_id1ykpE00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology130 — Protocatechuate 3,4-Dioxygenase, subunit A
Homologous superfamily homologous superfamily10 — Aromatic compound dioxygenase
Domain ID domain_id1ykpF00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology130 — Protocatechuate 3,4-Dioxygenase, subunit A
Homologous superfamily homologous superfamily10 — Aromatic compound dioxygenase
Domain ID domain_id1ykpG00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology130 — Protocatechuate 3,4-Dioxygenase, subunit A
Homologous superfamily homologous superfamily10 — Aromatic compound dioxygenase
Domain ID domain_id1ykpH00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology130 — Protocatechuate 3,4-Dioxygenase, subunit A
Homologous superfamily homologous superfamily10 — Aromatic compound dioxygenase
Domain ID domain_id1ykpI00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology130 — Protocatechuate 3,4-Dioxygenase, subunit A
Homologous superfamily homologous superfamily10 — Aromatic compound dioxygenase
Domain ID domain_id1ykpJ00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology130 — Protocatechuate 3,4-Dioxygenase, subunit A
Homologous superfamily homologous superfamily10 — Aromatic compound dioxygenase
Domain ID domain_id1ykpK00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology130 — Protocatechuate 3,4-Dioxygenase, subunit A
Homologous superfamily homologous superfamily10 — Aromatic compound dioxygenase
Domain ID domain_id1ykpL00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology130 — Protocatechuate 3,4-Dioxygenase, subunit A
Homologous superfamily homologous superfamily10 — Aromatic compound dioxygenase
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7. Citations (1)