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3pcm

STRUCTURE OF PROTOCATECHUATE 3,4-DIOXYGENASE COMPLEXED WITH 6-HYDROXYNICOTINIC ACID N-OXIDE AND CYANIDE

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

PROTOCATECHUATE 3,4-DIOXYGENASE

OrganismNot specified

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 × 12 （P00437） CYANIDE ION × 12 FE (III) ION × 12 6-HYDROXYISONICOTINIC ACID N-OXIDE × 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 B； PDBConstruct 1–200； UniProt 1–200 Author chain C； PDBConstruct 1–200； UniProt 1–200 Author chain D； PDBConstruct 1–200； UniProt 1–200 Author chain E； PDBConstruct 1–200； UniProt 1–200 Author chain F； PDBConstruct 1–200； UniProt 1–200

PROTOCATECHUATE 3,4-DIOXYGENASE

OrganismNot specified

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 × 12 （P00436） CYANIDE ION × 12 FE (III) ION × 12 6-HYDROXYISONICOTINIC ACID N-OXIDE × 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 M； PDBConstruct 1–238； UniProt 1–238 Author chain N； PDBConstruct 1–238； UniProt 1–238 Author chain O； PDBConstruct 1–238； UniProt 1–238 Author chain P； PDBConstruct 1–238； UniProt 1–238 Author chain Q； PDBConstruct 1–238； UniProt 1–238 Author chain R； 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_id3pcm
Deposition date deposition_date1997-07-18
Structure title titleSTRUCTURE OF PROTOCATECHUATE 3,4-DIOXYGENASE COMPLEXED WITH 6-HYDROXYNICOTINIC ACID N-OXIDE AND CYANIDE
Keywords keywordsDIOXYGENASE, IRON, NONHEME, METALLOPROTEIN, OXIDOREDUCTASE, TRANSITION-STATE ANALOG COMPLEX; DIOXYGENASE
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.

3pcm__assembly_1__model_1

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

Download this curve (.dat)

3pcm__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.

3pcm__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）54.14 Å
Rg (electron density)53.07 Å
Total Rg53.29 Å
Atom count41100
Residues5196
Excluded volume723490 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 3pcm__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 (6)

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6. Fold Classification (SCOP + CATH) 24 domains

SCOP 2.08 (12 domains)

Domain ID domain_idd3pcma_
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_idd3pcmb_
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_idd3pcmc_
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_idd3pcmd_
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_idd3pcme_
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_idd3pcmf_
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_idd3pcmm_
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_idd3pcmn_
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_idd3pcmo_
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_idd3pcmp_
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_idd3pcmq_
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_idd3pcmr_
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_id3pcmA00
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_id3pcmB00
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_id3pcmC00
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_id3pcmD00
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_id3pcmE00
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_id3pcmF00
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_id3pcmM00
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_id3pcmN00
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_id3pcmO00
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_id3pcmP00
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_id3pcmQ00
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_id3pcmR00
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 (4)