SAXSdb — 2ad7

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

Methanol dehydrogenase subunit 1

OrganismNot specified

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	Methanol dehydrogenase subunit 2 × 2 （P38540） CALCIUM ION × 2 PYRROLOQUINOLINE QUINONE × 2 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	DHM1_METME
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–571； UniProt 3–573 Author chain C； PDBConstruct 1–571； UniProt 3–573

Methanol dehydrogenase subunit 2

OrganismNot specified

UniProt P38540

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	Methanol dehydrogenase subunit 1 × 2 （P38539） CALCIUM ION × 2 PYRROLOQUINOLINE QUINONE × 2 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	DHM2_METME
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–69； UniProt 23–91 Author chain D； PDBConstruct 1–69； UniProt 23–91

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	2ad7
Deposition date deposition_date	2005-07-20
Structure title title	crystal structure of methanol dehydrogenase from M. W3A1 (form C) in the presence of methanol
Keywords keywords	methanol dehydrogenase, PQQ configuration, methanol, Oxidoreductase; 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.

2ad7__assembly_1__model_1

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

Download this curve (.dat)

2ad7__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2ad7__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	34.46 Å
Rg (electron density)	33.93 Å
Total Rg	34.44 Å
Atom count	9944
Residues	1280
Excluded volume	175810 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2ad7__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 (5)

Entity 1 Entity 1 polymer

Description description	Methanol dehydrogenase subunit 1
Molecular weight formula_weight	62500.6 kDa
EC 编号 ec_number	1.1.99.8
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C
Atom count atom_count	12004

DADLDKQVNTAGAWPIATGGYYSQHNSPLAQINKSNVKNVKAAWSFSTGVLNGHEGAPLVIGDMMYVHSAFPNNTYALNLNDPGKIVWQHKPKQDASTKAVMCCDVVDRGLAYGAGQIVKKQANGHLLALDAKTGKINWEVEVCDPKVGSTLTQAPFVAKDTVLMGCSGAELGVRGAVNAFDLKTGELKWRAFATGSDDSVRLAKDFNSANPHYGQFGLGTKTWEGDAWKIGGGTNWGWYAYDPKLNLFYYGSGNPAPWNETMRPGDNKWTMTIWGRDLDTGMAKWGYQKTPHDEWDFAGVNQMVLTDQPVNGKMTPLLSHIDRNGILYTLNRENGNLIVAEKVDPAVNVFKKVDLKTGTPVRDPEFATRMDHKGTNICPSAMGFHNQGVDSYDPESRTLYAGLNHICMDWEPFMLPYRAGQFFVGATLAMYPGPNGPTKKEMGQIRAFDLTTGKAKWTKWEKFAAWGGTLYTKGGLVWYATLDGYLKALDNKDGKELWNFKMPSGGIGSPMTYSFKGKQYIGSMYGVGGWPGVGLVFDLTDPSAGLGAVGAFRELQNHTQMGGGLMVFSL

Entity 2 Entity 2 polymer

Description description	Methanol dehydrogenase subunit 2
Molecular weight formula_weight	7770.6 kDa
EC 编号 ec_number	1.1.99.8
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

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

YDGQNCKEPGNCWENKPGYPEKIAGSKYDPKHDPVELNKQEESIKAMDARNAKRIANAKSSGNFVFDVK

Entity 3 Entity 3 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	PYRROLOQUINOLINE QUINONE
Molecular weight formula_weight	330.2 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	2060

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6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d2ad7a_
Class class	b — All beta proteins
Fold Fold fold	b.70 — 8-bladed beta-propeller
Superfamily Superfamily superfamily	b.70.1 — Quinoprotein alcohol dehydrogenase-like
Family Family family	b.70.1.1 — Quinoprotein alcohol dehydrogenase-like

Domain ID domain_id	d2ad7b_
Class class	a — All alpha proteins
Fold Fold fold	a.137 — Non-globular all-alpha subunits of globular proteins
Superfamily Superfamily superfamily	a.137.2 — Methanol dehydrogenase subunit
Family Family family	a.137.2.1 — Methanol dehydrogenase subunit

Domain ID domain_id	d2ad7c_
Class class	b — All beta proteins
Fold Fold fold	b.70 — 8-bladed beta-propeller
Superfamily Superfamily superfamily	b.70.1 — Quinoprotein alcohol dehydrogenase-like
Family Family family	b.70.1.1 — Quinoprotein alcohol dehydrogenase-like

Domain ID domain_id	d2ad7d_
Class class	a — All alpha proteins
Fold Fold fold	a.137 — Non-globular all-alpha subunits of globular proteins
Superfamily Superfamily superfamily	a.137.2 — Methanol dehydrogenase subunit
Family Family family	a.137.2.1 — Methanol dehydrogenase subunit

CATH v4.4 (4 domains)

Domain ID domain_id	2ad7A00
Class class	2 — Mainly Beta
Architecture architecture	140 — 8 Propeller
Topology topology	10 — Methanol Dehydrogenase; Chain A
Homologous superfamily homologous superfamily	10 — Quinoprotein alcohol dehydrogenase-like superfamily

Domain ID domain_id	2ad7B00
Class class	4 — Few Secondary Structures
Architecture architecture	10 — Irregular
Topology topology	160 — Methanol Dehydrogenase; Chain B
Homologous superfamily homologous superfamily	10 — Methanol dehydrogenase, beta subunit

Domain ID domain_id	2ad7C00
Class class	2 — Mainly Beta
Architecture architecture	140 — 8 Propeller
Topology topology	10 — Methanol Dehydrogenase; Chain A
Homologous superfamily homologous superfamily	10 — Quinoprotein alcohol dehydrogenase-like superfamily

Domain ID domain_id	2ad7D00
Class class	4 — Few Secondary Structures
Architecture architecture	10 — Irregular
Topology topology	160 — Methanol Dehydrogenase; Chain B
Homologous superfamily homologous superfamily	10 — Methanol dehydrogenase, beta subunit

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Unit-cell length a length_a	201.557 Å
Unit-cell length b length_b	61.889 Å
Unit-cell length c length_c	123.816 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	123.25 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	1.500 Å
Low-resolution limit resolution_low	41.740 Å
R factor r_factor	0.1560
R_work r_work	0.1560
R_free r_free	0.1770

crystal structure of methanol dehydrogenase from M. W3A1 (form C) in the presence of methanol

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

Methanol dehydrogenase subunit 1

State in the Current Structure

Other States of the Same Protein in the Database

Methanol dehydrogenase subunit 2

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

2ad7__assembly_1__model_1

2ad7__assembly_1__model_1 | I(q)

2ad7__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 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)

crystal structure of methanol dehydrogenase from M. W3A1 (form C) in the presence of methanol

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

Methanol dehydrogenase subunit 1

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Methanol dehydrogenase subunit 2

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

2ad7__assembly_1__model_1

2ad7__assembly_1__model_1 | I(q)

2ad7__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 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)