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2c3p

CRYSTAL STRUCTURE OF THE FREE RADICAL INTERMEDIATE OF PYRUVATE:FERREDOXIN OXIDOREDUCTASE FROM Desulfovibrio africanus

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

PYRUVATE-FERREDOXIN OXIDOREDUCTASE

OrganismNot specified

UniProt P94692

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein homooligomer Homooligomer Protein 2 IRON/SULFUR CLUSTER × 6 ;1-(2-{(2S,4R,5R)-3-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-2-[(1S)-1-CARBOXY-1-HYDROXYETHYL]-4-METHYL-1,3-THIAZOLIDIN-5-YL}ETHOXY)-1,1,3,3-TETRAHYDROXY-1LAMBDA~5~-DIPHOSPHOX-1-EN-2-IUM 3-OXIDE ; × 2 MAGNESIUM ION × 2 CALCIUM ION × 2 water × 2 Consistent with protein count

Other States of the Same Protein in the Database

Monomer

None

Homodimer
1b0p 1kek 2c3m 2c3o 2c3p 2c3u 2c3y 2c42 2pda 2uza 7plm

11 assemblies

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex

None

View Construct and Data Evidence
UniProt name P94692_DESAF
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–1231； UniProt 2–1232 Author chain B； PDBConstruct 1–1231； UniProt 2–1232

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_id2c3p
Deposition date deposition_date2005-10-11
Structure title titleCRYSTAL STRUCTURE OF THE FREE RADICAL INTERMEDIATE OF PYRUVATE:FERREDOXIN OXIDOREDUCTASE FROM Desulfovibrio africanus
Keywords keywords;OXIDOREDUCTASE, 4FE-4S, IRON, IRON-SULFUR, IRON-SULFUR CLUSTER, PYRUVATE CATABOLISM, TPP-DEPENDENT ENZYME, METAL-BINDING, ELECTRON TRANSPORT ;; 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.

2c3p__assembly_1__model_1

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

Download this curve (.dat)

2c3p__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.

2c3p__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）38.94 Å
Rg (electron density)38.51 Å
Total Rg39.01 Å
Atom count18882
Residues2462
Excluded volume336530 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 2c3p__assembly_1__model_1 dimeric （2） 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 (10 domains)

Domain ID domain_idd2c3pa1
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.36.1.8 — PFOR Pyr module
Domain ID domain_idd2c3pa2
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.36.1.12 — PFOR PP module
Domain ID domain_idd2c3pa3
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.48 — TK C-terminal domain-like
Superfamily Superfamily superfamilyc.48.1 — TK C-terminal domain-like
Family Family familyc.48.1.3 — Pyruvate-ferredoxin oxidoreductase, PFOR, domain II
Domain ID domain_idd2c3pa4
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.64 — Pyruvate-ferredoxin oxidoreductase, PFOR, domain III
Superfamily Superfamily superfamilyc.64.1 — Pyruvate-ferredoxin oxidoreductase, PFOR, domain III
Family Family familyc.64.1.1 — Pyruvate-ferredoxin oxidoreductase, PFOR, domain III
Domain ID domain_idd2c3pa5
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.58 — Ferredoxin-like
Superfamily Superfamily superfamilyd.58.1 — 4Fe-4S ferredoxins
Family Family familyd.58.1.5 — Ferredoxin domains from multidomain proteins
Domain ID domain_idd2c3pb1
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.36.1.8 — PFOR Pyr module
Domain ID domain_idd2c3pb2
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.36.1.12 — PFOR PP module
Domain ID domain_idd2c3pb3
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.48 — TK C-terminal domain-like
Superfamily Superfamily superfamilyc.48.1 — TK C-terminal domain-like
Family Family familyc.48.1.3 — Pyruvate-ferredoxin oxidoreductase, PFOR, domain II
Domain ID domain_idd2c3pb4
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.64 — Pyruvate-ferredoxin oxidoreductase, PFOR, domain III
Superfamily Superfamily superfamilyc.64.1 — Pyruvate-ferredoxin oxidoreductase, PFOR, domain III
Family Family familyc.64.1.1 — Pyruvate-ferredoxin oxidoreductase, PFOR, domain III
Domain ID domain_idd2c3pb5
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.58 — Ferredoxin-like
Superfamily Superfamily superfamilyd.58.1 — 4Fe-4S ferredoxins
Family Family familyd.58.1.5 — Ferredoxin domains from multidomain proteins

CATH v4.4 (14 domains)

Domain ID domain_id2c3pA01
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_id2c3pA02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily920 —
Domain ID domain_id2c3pA03
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology920 — Pyruvate-ferredoxin Oxidoreductase; domain 3
Homologous superfamily homologous superfamily10 — Pyruvate-ferredoxin oxidoreductase, PFOR, domain III
Domain ID domain_id2c3pA04
Class class4 — Few Secondary Structures
Architecture architecture10 — Irregular
Topology topology780 — Pyruvate-ferredoxin Oxidoreductase; domain 4
Homologous superfamily homologous superfamily10 — Pyruvate-flavodoxin oxidoreductase, EKR domain
Domain ID domain_id2c3pA05
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily20 —
Domain ID domain_id2c3pA06
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_id2c3pA07
Class class4 — Few Secondary Structures
Architecture architecture10 — Irregular
Topology topology790 — Pyruvate-ferredoxin Oxidoreductase; domain 7
Homologous superfamily homologous superfamily10 — Pyruvate-ferredoxin Oxidoreductase; domain 7
Domain ID domain_id2c3pB01
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_id2c3pB02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily920 —
Domain ID domain_id2c3pB03
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology920 — Pyruvate-ferredoxin Oxidoreductase; domain 3
Homologous superfamily homologous superfamily10 — Pyruvate-ferredoxin oxidoreductase, PFOR, domain III
Domain ID domain_id2c3pB04
Class class4 — Few Secondary Structures
Architecture architecture10 — Irregular
Topology topology780 — Pyruvate-ferredoxin Oxidoreductase; domain 4
Homologous superfamily homologous superfamily10 — Pyruvate-flavodoxin oxidoreductase, EKR domain
Domain ID domain_id2c3pB05
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily20 —
Domain ID domain_id2c3pB06
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_id2c3pB07
Class class4 — Few Secondary Structures
Architecture architecture10 — Irregular
Topology topology790 — Pyruvate-ferredoxin Oxidoreductase; domain 7
Homologous superfamily homologous superfamily10 — Pyruvate-ferredoxin Oxidoreductase; domain 7
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7. Citations (2)