1jmx

crystal structure of a quinohemoprotein amine dehydrogenase from pseudomonas putida

Method: X-RAY DIFFRACTION

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

Amine Dehydrogenase

OrganismNot specified

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	Amine Dehydrogenase × 1 （Q8VW82） Amine Dehydrogenase × 1 （P0A182） NICKEL (II) ION × 1 HEME C × 2 water × 3	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 6	Amine Dehydrogenase × 2 （Q8VW82） Amine Dehydrogenase × 2 （P0A182） NICKEL (II) ION × 2 HEME C × 4 water × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q8VW85_PSEPU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–494； UniProt 49–542

Amine Dehydrogenase

OrganismNot specified

UniProt Q8VW82

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	Amine Dehydrogenase × 1 （Q8VW85） Amine Dehydrogenase × 1 （P0A182） NICKEL (II) ION × 1 HEME C × 2 water × 3	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 6	Amine Dehydrogenase × 2 （Q8VW85） Amine Dehydrogenase × 2 （P0A182） NICKEL (II) ION × 2 HEME C × 4 water × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q8VW82_PSEPU
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–349； UniProt 31–379

Amine Dehydrogenase

OrganismNot specified

UniProt P0A182

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	Amine Dehydrogenase × 1 （Q8VW85） Amine Dehydrogenase × 1 （Q8VW82） NICKEL (II) ION × 1 HEME C × 2 water × 3	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 6	Amine Dehydrogenase × 2 （Q8VW85） Amine Dehydrogenase × 2 （Q8VW82） NICKEL (II) ION × 2 HEME C × 4 water × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	QADG_PSEPU
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain G； PDBConstruct 2–79； UniProt 1–78

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	1jmx
Deposition date deposition_date	2001-07-20
Structure title title	crystal structure of a quinohemoprotein amine dehydrogenase from pseudomonas putida
Keywords keywords	Amine Dehydrogenase, 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.

1jmx__assembly_2__model_1

Assembly 2 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

1jmx__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1jmx__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	42.86 Å
Rg (electron density)	43.02 Å
Total Rg	43.27 Å
Atom count	14308
Residues	1816
Excluded volume	253310 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1jmx__assembly_1__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1jmx__assembly_2__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 (6)

Entity 1 Entity 1 polymer

Description description	Amine Dehydrogenase
Molecular weight formula_weight	53986.9 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	7611

AEQGPSLLQNKCMGCHIPEGNDTYSRISHQRKTPEGWLMSIARMQVMHGLQISDDDRRTLVKYLADKQGLAPSETDGVRYAMERRLNTVEQFDTQLSETCGRCHSGARVALQRRPAKEWEHLVNFHLGQWPSLEYQAQARDRDWLPIALQQVVPDLAKRYPLESAAWAEWQKARPKADALPGQWAFSGHMLAKGDVRGVMSVTPDQGDTFKVEVKGAYADGTPFNGSGSAILYNGYEWRGNVKVGDANLRQVFAALDGEMKGRMFEAEHDERGLDFTAVKEGKARLLAVQPAFIKAGGESEITLVGSGLAGKPDLGAGVEVTEVLEQTPTLVRLKARAAADAKPGQREVAVGTLKGVNLAVYDKVEEVKVVPAFSIARIGENGASVPKVQGRFEAEAWGKDANGQPLRIGYLPASWKVEPFNERAVEDEDVKFAGKMQADGVFVPGGAGPNPERKMMTNNAGNLKVIATLADGGQTGEGHMIVTVQRWNNPPLP

Entity 2 Entity 2 polymer

Description description	Amine Dehydrogenase
Molecular weight formula_weight	39284.6 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

ADTGPALKAGHEYMIVTNYPNNLHVVDVASDTVYKSCVMPDKFGPGTAMMAPDNRTAYVLNNHYGDIYGIDLDTCKNTFHANLSSVPGEVGRSMYSFAISPDGKEVYATVNPTQRLNDHYVVKPPRLEVFSTADGLEAKPVRTFPMPRQVYLMRAADDGSLYVAGPDIYKMDVKTGKYTVALPLRNWNRKGYSAPDVLYFWPHQSPRHEFSMLYTIARFKDDKQDPATADLLYGYLSVDLKTGKTHTQEFADLTELYFTGLRSPKDPNQIYGVLNRLAKYDLKQRKLIKAANLDHTYYCVAFDKKGDKLYLGGTFNDLAVFNPDTLEKVKNIKLPGGDMSTTTPQVFIR

Entity 3 Entity 3 polymer

Description description	Amine Dehydrogenase
Molecular weight formula_weight	8630.4 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	G

MSAVAGCTATTDPGWEVDAFGGVSSLCQPMEADLYGCSDPCWWPAQVPDMMSTYQDWNAQASNSAEDWRNLGTVFPKDK

Entity 4 Entity 4 non-polymer

Description description	NICKEL (II) ION
Molecular weight formula_weight	58.7 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 non-polymer

Description description	HEME C
Molecular weight formula_weight	618.5 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	457

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6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (7 domains)

Domain ID domain_id	d1jmxa1
Class class	a — All alpha proteins
Fold Fold fold	a.3 — Cytochrome c
Superfamily Superfamily superfamily	a.3.1 — Cytochrome c
Family Family family	a.3.1.7 — Quinohemoprotein amine dehydrogenase A chain, domains 1 and 2

Domain ID domain_id	d1jmxa2
Class class	a — All alpha proteins
Fold Fold fold	a.3 — Cytochrome c
Superfamily Superfamily superfamily	a.3.1 — Cytochrome c
Family Family family	a.3.1.7 — Quinohemoprotein amine dehydrogenase A chain, domains 1 and 2

Domain ID domain_id	d1jmxa3
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.18 — E set domains
Family Family family	b.1.18.14 — Quinohemoprotein amine dehydrogenase A chain, domains 4 and 5

Domain ID domain_id	d1jmxa4
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.18 — E set domains
Family Family family	b.1.18.14 — Quinohemoprotein amine dehydrogenase A chain, domains 4 and 5

Domain ID domain_id	d1jmxa5
Class class	b — All beta proteins
Fold Fold fold	b.61 — Streptavidin-like
Superfamily Superfamily superfamily	b.61.4 — Quinohemoprotein amine dehydrogenase A chain, domain 3
Family Family family	b.61.4.1 — Quinohemoprotein amine dehydrogenase A chain, domain 3

Domain ID domain_id	d1jmxb_
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.69.2.2 — Quinohemoprotein amine dehydrogenase B chain

Domain ID domain_id	d1jmxg_
Class class	a — All alpha proteins
Fold Fold fold	a.137 — Non-globular all-alpha subunits of globular proteins
Superfamily Superfamily superfamily	a.137.9 — Quinohemoprotein amine dehydrogenase C chain
Family Family family	a.137.9.1 — Quinohemoprotein amine dehydrogenase C chain

CATH v4.4 (5 domains)

Domain ID domain_id	1jmxA02
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	128 — Lipocalin
Homologous superfamily homologous superfamily	120 — Quinohemoprotein amine dehydrogenase alpha subunit, domain 2

Domain ID domain_id	1jmxA03
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	1jmxA04
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	1jmxB00
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	1jmxG00
Class class	4 — Few Secondary Structures
Architecture architecture	10 — Irregular
Topology topology	940 — Quinohemoprotein amine dehydrogenase
Homologous superfamily homologous superfamily	10 — Quinohemoprotein amine dehydrogenase, gamma subunit structural domain

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Unit-cell length a length_a	167.210 Å
Unit-cell length b length_b	92.370 Å
Unit-cell length c length_c	79.300 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	112.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

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

Resolution resolution	1.900 Å
Low-resolution limit resolution_low	10.000 Å
R factor r_factor	—
R_work r_work	0.2090
R_free r_free	0.2670

crystal structure of a quinohemoprotein amine dehydrogenase from pseudomonas putida

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

Amine Dehydrogenase

State in the Current Structure

Other States of the Same Protein in the Database

Amine Dehydrogenase

State in the Current Structure

Other States of the Same Protein in the Database

Amine Dehydrogenase

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

1jmx__assembly_2__model_1

1jmx__assembly_2__model_1 | I(q)

1jmx__assembly_2__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 (6)

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 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (7 domains)

CATH v4.4 (5 domains)

7. Citations (1)

crystal structure of a quinohemoprotein amine dehydrogenase from pseudomonas putida

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

Amine Dehydrogenase

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Amine Dehydrogenase

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Amine Dehydrogenase

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

1jmx__assembly_2__model_1

1jmx__assembly_2__model_1 | I(q)

1jmx__assembly_2__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 (6)

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 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (7 domains)

CATH v4.4 (5 domains)

7. Citations (1)