SAXSdb — 2mad

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

METHYLAMINE DEHYDROGENASE (LIGHT SUBUNIT)

Paracoccus versutus

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 SUBUNIT) × 2 （P23006） water × 2	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	1
Chains and sequence ranges	Author chain L； PDBConstruct 1–124； UniProt 64–187

METHYLAMINE DEHYDROGENASE (HEAVY SUBUNIT)

Paracoccus versutus

UniProt P23006

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 SUBUNIT) × 2 （P22641） water × 2	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	2
Chains and sequence ranges	Author chain H； PDBConstruct 7–348； UniProt 59–400

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	2mad
Deposition date deposition_date	1992-05-20
Structure title title	THE ACTIVE SITE STRUCTURE OF METHYLAMINE DEHYDROGENASE: HYDRAZINES IDENTIFY C6 AS THE REACTIVE SITE OF THE TRYPTOPHAN DERIVED QUINONE COFACTOR
Keywords keywords	OXIDOREDUCTASE(CHNH2(D)-DEAMINATING); OXIDOREDUCTASE(CHNH2(D)-DEAMINATING)
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.

2mad__assembly_1__model_1

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

Download this curve (.dat)

2mad__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2mad__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	29.69 Å
Rg (electron density)	29.11 Å
Total Rg	30.86 Å
Atom count	1904
Residues	246
Excluded volume	125700 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2mad__assembly_1__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 (3)

Entity 1 Entity 1 polymer

Description description	METHYLAMINE DEHYDROGENASE (LIGHT SUBUNIT)
Molecular weight formula_weight	13668.2 kDa
EC 编号 ec_number	1.4.99.3
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	L
Atom count atom_count	1411

VDPRAKWQPQDNDIQACDYWRHCSIDGNICDCSGGSLTNCPPGTKLATASWVASCYNPTDGQSYLIAYRDCCGYNVSGRCPCLNTEGELPVYRPEFANDIIWCFGAEDDAMTYHCTISPIVGKA

Source Source

Source organism organism	Paracoccus versutus
NCBI taxonomy ID ncbi_taxonomy_id	34007

Entity 2 Entity 2 polymer

Description description	METHYLAMINE DEHYDROGENASE (HEAVY SUBUNIT)
Molecular weight formula_weight	38032.0 kDa
EC 编号 ec_number	1.4.99.3
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	H

SSASAAAAAAAAALAAGAADGPTNDEAPGADGRRSYINLPAHHSAIIQQWVLDAGSGSILGHVNGGFLPNPVAAHSGSEFALASTSFSRIAKGKRTDYVEVFDPVTFLPIADIELPDAPRFDVGPYSWMNANTPNNADLLFFQFAAGPAVGLVVQGGSSDDQLLSSPTCYHIHPGAPSTFYLLCAQGGLAKTDHAGGAAGAGLVGAMLTAAQNLLTQPAQANKSGRIVWPVYSGKILQADISAAGATNKAPIDALSGGRKADTWRPGGWQQVAYLKSSDGIYLLTSEQSAWKLHAAAKEVTSVTGLVGQTSSQISLGHDVDAISVAQDGGPDLYALSAGTEVLHIYDAGAGDQDQSTVELGSGPQVLSVMNEA

Source Source

Source organism organism	Paracoccus versutus
NCBI taxonomy ID ncbi_taxonomy_id	34007

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	86

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6. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d2madh_
Class class	b — All beta proteins
Fold Fold fold	b.69 — 7-bladed beta-propeller
Superfamily Superfamily superfamily	b.69.2 — YVTN repeat-like/Quinoprotein amine dehydrogenase
Family Family family	b.69.2.1 — Methylamine dehydrogenase, H-chain

Domain ID domain_id	d2madl_
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 (1 domains)

Domain ID domain_id	2madL00
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	129.784 Å
Unit-cell length b length_b	129.784 Å
Unit-cell length c length_c	104.334 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	6

Space group space_group	P 31 2 1
Space-group number int_tables_number	152
Crystal system crystal_system	—

Resolution resolution	2.250 Å
Low-resolution limit resolution_low	— Å
R factor r_factor	0.2090
R_work r_work	—
R_free r_free	—

THE ACTIVE SITE STRUCTURE OF METHYLAMINE DEHYDROGENASE: HYDRAZINES IDENTIFY C6 AS THE REACTIVE SITE OF THE TRYPTOPHAN DERIVED QUINONE COFACTOR

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

METHYLAMINE DEHYDROGENASE (LIGHT SUBUNIT)

State in the Current Structure

Other States of the Same Protein in the Database

METHYLAMINE DEHYDROGENASE (HEAVY SUBUNIT)

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

2mad__assembly_1__model_1

2mad__assembly_1__model_1 | I(q)

2mad__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (2 domains)

CATH v4.4 (1 domains)

7. Citations (4)

THE ACTIVE SITE STRUCTURE OF METHYLAMINE DEHYDROGENASE: HYDRAZINES IDENTIFY C6 AS THE REACTIVE SITE OF THE TRYPTOPHAN DERIVED QUINONE COFACTOR

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

METHYLAMINE DEHYDROGENASE (LIGHT SUBUNIT)

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 (HEAVY SUBUNIT)

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

2mad__assembly_1__model_1

2mad__assembly_1__model_1 | I(q)

2mad__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (2 domains)

CATH v4.4 (1 domains)

7. Citations (4)