2gc4

Structural comparison of the oxidized ternary electron transfer complex of methylamine dehydrogenase, amicyanin and cytochrome c551i from Paracoccus denitrificans with the substrate-reduced, copper free complex at 1.9 A resolution.

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

Methylamine dehydrogenase heavy chain

OrganismNot specified

UniProt P29894

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 4 Methylamine dehydrogenase light chain × 1 (P22619) Amicyanin × 1 (P22364) Cytochrome c-L × 1 (P29899) COPPER (II) ION × 1 SODIUM ION × 1 HEME C × 1 water × 4 Consistent with protein count
2 Protein heterocomplex Heteromer Protein 4 Methylamine dehydrogenase light chain × 1 (P22619) Amicyanin × 1 (P22364) Cytochrome c-L × 1 (P29899) COPPER (II) ION × 1 SODIUM ION × 1 HEME C × 1 water × 4 Consistent with protein count
3 Protein heterocomplex Heteromer Protein 4 Methylamine dehydrogenase light chain × 1 (P22619) Amicyanin × 1 (P22364) Cytochrome c-L × 1 (P29899) COPPER (II) ION × 1 SODIUM ION × 1 HEME C × 1 water × 4 Consistent with protein count
4 Protein heterocomplex Heteromer Protein 4 Methylamine dehydrogenase light chain × 1 (P22619) Amicyanin × 1 (P22364) Cytochrome c-L × 1 (P29899) COPPER (II) ION × 1 SODIUM ION × 1 HEME C × 1 water × 4 Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence
UniProt name DHMH_PARDE
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–386; UniProt 32–417 Author chain E; PDBConstruct 1–386; UniProt 32–417 Author chain I; PDBConstruct 1–386; UniProt 32–417 Author chain M; PDBConstruct 1–386; UniProt 32–417

Methylamine dehydrogenase light chain

OrganismNot specified

UniProt P22619

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 4 Methylamine dehydrogenase heavy chain × 1 (P29894) Amicyanin × 1 (P22364) Cytochrome c-L × 1 (P29899) COPPER (II) ION × 1 SODIUM ION × 1 HEME C × 1 water × 4 Consistent with protein count
2 Protein heterocomplex Heteromer Protein 4 Methylamine dehydrogenase heavy chain × 1 (P29894) Amicyanin × 1 (P22364) Cytochrome c-L × 1 (P29899) COPPER (II) ION × 1 SODIUM ION × 1 HEME C × 1 water × 4 Consistent with protein count
3 Protein heterocomplex Heteromer Protein 4 Methylamine dehydrogenase heavy chain × 1 (P29894) Amicyanin × 1 (P22364) Cytochrome c-L × 1 (P29899) COPPER (II) ION × 1 SODIUM ION × 1 HEME C × 1 water × 4 Consistent with protein count
4 Protein heterocomplex Heteromer Protein 4 Methylamine dehydrogenase heavy chain × 1 (P29894) Amicyanin × 1 (P22364) Cytochrome c-L × 1 (P29899) COPPER (II) ION × 1 SODIUM ION × 1 HEME C × 1 water × 4 Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence
UniProt name DHML_PARDE
Isoform —
PDB entities 2
Chains and sequence ranges Author chain B; PDBConstruct 1–131; UniProt 58–188 Author chain F; PDBConstruct 1–131; UniProt 58–188 Author chain J; PDBConstruct 1–131; UniProt 58–188 Author chain N; PDBConstruct 1–131; UniProt 58–188

Amicyanin

OrganismNot specified

UniProt P22364

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 4 Methylamine dehydrogenase heavy chain × 1 (P29894) Methylamine dehydrogenase light chain × 1 (P22619) Cytochrome c-L × 1 (P29899) COPPER (II) ION × 1 SODIUM ION × 1 HEME C × 1 water × 4 Consistent with protein count
2 Protein heterocomplex Heteromer Protein 4 Methylamine dehydrogenase heavy chain × 1 (P29894) Methylamine dehydrogenase light chain × 1 (P22619) Cytochrome c-L × 1 (P29899) COPPER (II) ION × 1 SODIUM ION × 1 HEME C × 1 water × 4 Consistent with protein count
3 Protein heterocomplex Heteromer Protein 4 Methylamine dehydrogenase heavy chain × 1 (P29894) Methylamine dehydrogenase light chain × 1 (P22619) Cytochrome c-L × 1 (P29899) COPPER (II) ION × 1 SODIUM ION × 1 HEME C × 1 water × 4 Consistent with protein count
4 Protein heterocomplex Heteromer Protein 4 Methylamine dehydrogenase heavy chain × 1 (P29894) Methylamine dehydrogenase light chain × 1 (P22619) Cytochrome c-L × 1 (P29899) COPPER (II) ION × 1 SODIUM ION × 1 HEME C × 1 water × 4 Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence
UniProt name AMCY_PARDE
Isoform —
PDB entities 3
Chains and sequence ranges Author chain C; PDBConstruct 1–105; UniProt 27–131 Author chain G; PDBConstruct 1–105; UniProt 27–131 Author chain K; PDBConstruct 1–105; UniProt 27–131 Author chain O; PDBConstruct 1–105; UniProt 27–131

Cytochrome c-L

OrganismNot specified

UniProt P29899

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 4 Methylamine dehydrogenase heavy chain × 1 (P29894) Methylamine dehydrogenase light chain × 1 (P22619) Amicyanin × 1 (P22364) COPPER (II) ION × 1 SODIUM ION × 1 HEME C × 1 water × 4 Consistent with protein count
2 Protein heterocomplex Heteromer Protein 4 Methylamine dehydrogenase heavy chain × 1 (P29894) Methylamine dehydrogenase light chain × 1 (P22619) Amicyanin × 1 (P22364) COPPER (II) ION × 1 SODIUM ION × 1 HEME C × 1 water × 4 Consistent with protein count
3 Protein heterocomplex Heteromer Protein 4 Methylamine dehydrogenase heavy chain × 1 (P29894) Methylamine dehydrogenase light chain × 1 (P22619) Amicyanin × 1 (P22364) COPPER (II) ION × 1 SODIUM ION × 1 HEME C × 1 water × 4 Consistent with protein count
4 Protein heterocomplex Heteromer Protein 4 Methylamine dehydrogenase heavy chain × 1 (P29894) Methylamine dehydrogenase light chain × 1 (P22619) Amicyanin × 1 (P22364) COPPER (II) ION × 1 SODIUM ION × 1 HEME C × 1 water × 4 Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence
UniProt name CYCL_PARDE
Isoform —
PDB entities 4
Chains and sequence ranges Author chain D; PDBConstruct 1–147; UniProt 23–169 Author chain H; PDBConstruct 1–147; UniProt 23–169 Author chain L; PDBConstruct 1–147; UniProt 23–169 Author chain P; PDBConstruct 1–147; UniProt 23–169

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_id2gc4
Deposition date deposition_date2006-03-13
Structure title titleStructural comparison of the oxidized ternary electron transfer complex of methylamine dehydrogenase, amicyanin and cytochrome c551i from Paracoccus denitrificans with the substrate-reduced, copper free complex at 1.9 A resolution.
Keywords keywordsElectron transfer, Methylamine dehydrogenase, Cytochrome, Blue copper protein, Oxidoreductase, Electron transport; Oxidoreductase, Electron transport
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.

2gc4__assembly_1__model_1

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

Download this curve (.dat)

2gc4__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.

2gc4__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)30.19 Å
Rg (electron density)29.52 Å
Total Rg30.11 Å
Atom count5920
Residues758
Excluded volume104210 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 2gc4__assembly_1__model_1 tetrameric (4) Success 4.1.3-1-20251215 (887e7ef) View Download
2 1 2gc4__assembly_2__model_1 tetrameric (4) Success 4.1.3-1-20251215 (887e7ef) View Download
3 1 2gc4__assembly_3__model_1 tetrameric (4) Success 4.1.3-1-20251215 (887e7ef) View Download
4 1 2gc4__assembly_4__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 (8)

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6. Fold Classification (SCOP + CATH) 32 domains

SCOP 2.08 (16 domains)

Domain ID domain_idd2gc4a_
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.69.2.0 — automated matches
Domain ID domain_idd2gc4b_
Class classg — Small proteins
Fold Fold foldg.21 — Methylamine dehydrogenase, L chain
Superfamily Superfamily superfamilyg.21.1 — Methylamine dehydrogenase, L chain
Family Family familyg.21.1.1 — Methylamine dehydrogenase, L chain
Domain ID domain_idd2gc4c_
Class classb — All beta proteins
Fold Fold foldb.6 — Cupredoxin-like
Superfamily Superfamily superfamilyb.6.1 — Cupredoxins
Family Family familyb.6.1.1 — Plastocyanin/azurin-like
Domain ID domain_idd2gc4d_
Class classa — All alpha proteins
Fold Fold folda.3 — Cytochrome c
Superfamily Superfamily superfamilya.3.1 — Cytochrome c
Family Family familya.3.1.1 — monodomain cytochrome c
Domain ID domain_idd2gc4e_
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.69.2.0 — automated matches
Domain ID domain_idd2gc4f_
Class classg — Small proteins
Fold Fold foldg.21 — Methylamine dehydrogenase, L chain
Superfamily Superfamily superfamilyg.21.1 — Methylamine dehydrogenase, L chain
Family Family familyg.21.1.1 — Methylamine dehydrogenase, L chain
Domain ID domain_idd2gc4g_
Class classb — All beta proteins
Fold Fold foldb.6 — Cupredoxin-like
Superfamily Superfamily superfamilyb.6.1 — Cupredoxins
Family Family familyb.6.1.1 — Plastocyanin/azurin-like
Domain ID domain_idd2gc4h_
Class classa — All alpha proteins
Fold Fold folda.3 — Cytochrome c
Superfamily Superfamily superfamilya.3.1 — Cytochrome c
Family Family familya.3.1.1 — monodomain cytochrome c
Domain ID domain_idd2gc4i_
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.69.2.0 — automated matches
Domain ID domain_idd2gc4j_
Class classg — Small proteins
Fold Fold foldg.21 — Methylamine dehydrogenase, L chain
Superfamily Superfamily superfamilyg.21.1 — Methylamine dehydrogenase, L chain
Family Family familyg.21.1.1 — Methylamine dehydrogenase, L chain
Domain ID domain_idd2gc4k_
Class classb — All beta proteins
Fold Fold foldb.6 — Cupredoxin-like
Superfamily Superfamily superfamilyb.6.1 — Cupredoxins
Family Family familyb.6.1.1 — Plastocyanin/azurin-like
Domain ID domain_idd2gc4l_
Class classa — All alpha proteins
Fold Fold folda.3 — Cytochrome c
Superfamily Superfamily superfamilya.3.1 — Cytochrome c
Family Family familya.3.1.1 — monodomain cytochrome c
Domain ID domain_idd2gc4m_
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.69.2.0 — automated matches
Domain ID domain_idd2gc4n_
Class classg — Small proteins
Fold Fold foldg.21 — Methylamine dehydrogenase, L chain
Superfamily Superfamily superfamilyg.21.1 — Methylamine dehydrogenase, L chain
Family Family familyg.21.1.1 — Methylamine dehydrogenase, L chain
Domain ID domain_idd2gc4o_
Class classb — All beta proteins
Fold Fold foldb.6 — Cupredoxin-like
Superfamily Superfamily superfamilyb.6.1 — Cupredoxins
Family Family familyb.6.1.1 — Plastocyanin/azurin-like
Domain ID domain_idd2gc4p_
Class classa — All alpha proteins
Fold Fold folda.3 — Cytochrome c
Superfamily Superfamily superfamilya.3.1 — Cytochrome c
Family Family familya.3.1.1 — monodomain cytochrome c

CATH v4.4 (16 domains)

Domain ID domain_id2gc4A00
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_id2gc4B00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology30 — Electron Transport Ethylamine Dehydrogenase
Homologous superfamily homologous superfamily10 — Methylamine/Aralkylamine dehydrogenase light chain
Domain ID domain_id2gc4C00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily420 — Cupredoxins - blue copper proteins
Domain ID domain_id2gc4D00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology760 — Cytochrome Bc1 Complex; Chain D, domain 2
Homologous superfamily homologous superfamily10 — Cytochrome c-like domain
Domain ID domain_id2gc4E00
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_id2gc4F00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology30 — Electron Transport Ethylamine Dehydrogenase
Homologous superfamily homologous superfamily10 — Methylamine/Aralkylamine dehydrogenase light chain
Domain ID domain_id2gc4G00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily420 — Cupredoxins - blue copper proteins
Domain ID domain_id2gc4H00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology760 — Cytochrome Bc1 Complex; Chain D, domain 2
Homologous superfamily homologous superfamily10 — Cytochrome c-like domain
Domain ID domain_id2gc4I00
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_id2gc4J00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology30 — Electron Transport Ethylamine Dehydrogenase
Homologous superfamily homologous superfamily10 — Methylamine/Aralkylamine dehydrogenase light chain
Domain ID domain_id2gc4K00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily420 — Cupredoxins - blue copper proteins
Domain ID domain_id2gc4L00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology760 — Cytochrome Bc1 Complex; Chain D, domain 2
Homologous superfamily homologous superfamily10 — Cytochrome c-like domain
Domain ID domain_id2gc4M00
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_id2gc4N00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology30 — Electron Transport Ethylamine Dehydrogenase
Homologous superfamily homologous superfamily10 — Methylamine/Aralkylamine dehydrogenase light chain
Domain ID domain_id2gc4O00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily420 — Cupredoxins - blue copper proteins
Domain ID domain_id2gc4P00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology760 — Cytochrome Bc1 Complex; Chain D, domain 2
Homologous superfamily homologous superfamily10 — Cytochrome c-like domain
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7. Citations (2)