SAXSdb — 3c75

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Methylamine dehydrogenase heavy chain

OrganismNot specified

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 6	Methylamine dehydrogenase light chain × 2 （P22641） Amicyanin × 2 （P22365） COPPER (II) ION × 2 water × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	DHMH_PARVE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain H； PDBConstruct 1–426； UniProt 1–426 Author chain J； PDBConstruct 1–426； UniProt 1–426

Methylamine dehydrogenase light chain

OrganismNot specified

UniProt P22641

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 6	Methylamine dehydrogenase heavy chain × 2 （P23006） Amicyanin × 2 （P22365） COPPER (II) ION × 2 water × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	DHML_PARVE
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain L； PDBConstruct 1–188； UniProt 1–188 Author chain M； PDBConstruct 1–188； UniProt 1–188

Amicyanin

OrganismNot specified

UniProt P22365

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 6	Methylamine dehydrogenase heavy chain × 2 （P23006） Methylamine dehydrogenase light chain × 2 （P22641） COPPER (II) ION × 2 water × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	AMCY_PARVE
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain A； PDBConstruct 1–132； UniProt 1–132 Author chain B； PDBConstruct 1–132； UniProt 1–132

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_id	3c75
Deposition date deposition_date	2008-02-06
Structure title title	Paracoccus versutus methylamine dehydrogenase in complex with amicyanin
Keywords keywords	;copper proteins, electron transfer complex, TTQ, Electron transport, Oxidoreductase, Periplasm, Transport, Metal-binding, Pyrrolidone carboxylic acid ;; OXIDOREDUCTASE
Experimental Method method	X-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.

3c75__assembly_1__model_1

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

Download this curve (.dat)

3c75__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3c75__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	32.85 Å
Rg (electron density)	32.19 Å
Total Rg	32.79 Å
Atom count	9410
Residues	1210
Excluded volume	165710 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3c75__assembly_1__model_1`	hexameric （6）	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)

Entity 1 Entity 1 polymer

Description description	Methylamine dehydrogenase heavy chain
Molecular weight formula_weight	46430.5 kDa
EC 编号 ec_number	1.4.99.3
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	H,J
Atom count atom_count	9803

MASARESTPRYLTLIGATLACSALALGAAQAQTEPAEPEAPAETAAADAAGQTEGQRGAAEAAAALAAGEADEPVILEAPAPDARRVYIQDPAHFAAITQQFVIDGSTGRILGMTDGGFLPHPVAAEDGSFFAQASTVFERIARGKRTDYVEVFDPVTFLPIADIELPDAPRFLVGTYQWMNALTPDNKNLLFYQFSPAPAVGVVDLEGKTFDRMLDVPDCYHIFPASPTVFYMNCRDGSLARVDFADGETKVTNTEVFHTEDELLINHPAFSLRSGRLVWPTYTGKIFQADLTAEGATFRAPIEALTEAERADDWRPGGWQQTAYHRQSDRIYLLVDQRDEWKHKAASRFVVVLNAETGERINKIELGHEIDSINVSQDAEPLLYALSAGTQTLHIYDAATGEELRSVDQLGRGPQIITTHDMDS

Entity 2 Entity 2 polymer

Description description	Methylamine dehydrogenase light chain
Molecular weight formula_weight	20410.0 kDa
EC 编号 ec_number	1.4.99.3
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	L,M

MLGNFRFDDMVEKLSRRVAGRTSRRGAIGRLGTVLAGAALVPLLPVDRRGRVSRANAAGPAEGVDPRAKWQPQDNDIQACDYWRHCSIDGNICDCSGGSLTNCPPGTKLATASWVASCYNPTDGQSYLIAYRDCCGYNVSGRCPCLNTEGELPVYRPEFANDIIWCFGAEDDAMTYHCTISPIVGKAS

Entity 3 Entity 3 polymer

Description description	Amicyanin
Molecular weight formula_weight	14273.5 kDa
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B

MISAKTLRPAIAAIALFAIGATGAWAQDKITVTSEKPVAAADVPADAVVVGIEKMKYLTPEVTIKAGETVYWVNGEVMPHNVAFKKGIVGEDAFRGEMMTKDQAYAITFNEAGSYDYFCTPHPFMRGKVIVE

Entity 4 Entity 4 non-polymer

Description description	COPPER (II) ION
Molecular weight formula_weight	63.5 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	393

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6. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d3c75a_
Class class	b — All beta proteins
Fold Fold fold	b.6 — Cupredoxin-like
Superfamily Superfamily superfamily	b.6.1 — Cupredoxins
Family Family family	b.6.1.1 — Plastocyanin/azurin-like

Domain ID domain_id	d3c75b_
Class class	b — All beta proteins
Fold Fold fold	b.6 — Cupredoxin-like
Superfamily Superfamily superfamily	b.6.1 — Cupredoxins
Family Family family	b.6.1.1 — Plastocyanin/azurin-like

Domain ID domain_id	d3c75l_
Class class	g — Small proteins
Fold Fold fold	g.21 — Methylamine dehydrogenase, L chain
Superfamily Superfamily superfamily	g.21.1 — Methylamine dehydrogenase, L chain
Family Family family	g.21.1.1 — Methylamine dehydrogenase, L chain

Domain ID domain_id	d3c75m_
Class class	g — Small proteins
Fold Fold fold	g.21 — Methylamine dehydrogenase, L chain
Superfamily Superfamily superfamily	g.21.1 — Methylamine dehydrogenase, L chain
Family Family family	g.21.1.1 — Methylamine dehydrogenase, L chain

CATH v4.4 (6 domains)

Domain ID domain_id	3c75A00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	420 — Cupredoxins - blue copper proteins

Domain ID domain_id	3c75B00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	420 — Cupredoxins - blue copper proteins

Domain ID domain_id	3c75H00
Class class	2 — Mainly Beta
Architecture architecture	130 — 7 Propeller
Topology topology	10 — Methylamine Dehydrogenase; Chain H
Homologous superfamily homologous superfamily	10 — YVTN repeat-like/Quinoprotein amine dehydrogenase

Domain ID domain_id	3c75J00
Class class	2 — Mainly Beta
Architecture architecture	130 — 7 Propeller
Topology topology	10 — Methylamine Dehydrogenase; Chain H
Homologous superfamily homologous superfamily	10 — YVTN repeat-like/Quinoprotein amine dehydrogenase

Domain ID domain_id	3c75L00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	30 — Electron Transport Ethylamine Dehydrogenase
Homologous superfamily homologous superfamily	10 — Methylamine/Aralkylamine dehydrogenase light chain

Domain ID domain_id	3c75M00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	30 — Electron Transport Ethylamine Dehydrogenase
Homologous superfamily homologous superfamily	10 — Methylamine/Aralkylamine dehydrogenase light chain

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Unit-cell length a length_a	55.573 Å
Unit-cell length b length_b	131.038 Å
Unit-cell length c length_c	171.689 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.500 Å
Low-resolution limit resolution_low	30.150 Å
R factor r_factor	0.2350
R_work r_work	0.2350
R_free r_free	0.2830

Paracoccus versutus methylamine dehydrogenase in complex with amicyanin

1. Protein Identity and Related Structures Protein Identity & Related Structures

Methylamine dehydrogenase heavy chain

State in the Current Structure

Other States of the Same Protein in the Database

Methylamine dehydrogenase light chain

State in the Current Structure

Other States of the Same Protein in the Database

Amicyanin

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

3c75__assembly_1__model_1

3c75__assembly_1__model_1 | I(q)

3c75__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (4 domains)

CATH v4.4 (6 domains)

7. Citations (1)

Paracoccus versutus methylamine dehydrogenase in complex with amicyanin

1. Protein Identity and Related Structures Protein Identity & Related Structures

Methylamine dehydrogenase heavy chain

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Methylamine dehydrogenase light chain

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Amicyanin

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

3c75__assembly_1__model_1

3c75__assembly_1__model_1 | I(q)

3c75__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (4 domains)

CATH v4.4 (6 domains)

7. Citations (1)