4hm3

Naphthalene 1,2-Dioxygenase bound to ethylbenzene

Method: X-RAY DIFFRACTION

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

Naphthalene 1,2-dioxygenase subunit alpha

Pseudomonas sp. C18

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 6	Naphthalene 1,2-dioxygenase subunit beta × 3 （P0A113） 1,2-ETHANEDIOL × 24 SULFATE ION × 12 FE2/S2 (INORGANIC) CLUSTER × 3 FE (III) ION × 3 PHENYLETHANE × 3 water × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	NDOB_PSEU8
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–449； UniProt 1–449

Naphthalene 1,2-dioxygenase subunit beta

Pseudomonas sp. C18

UniProt P0A113

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 6	Naphthalene 1,2-dioxygenase subunit alpha × 3 （P0A111） 1,2-ETHANEDIOL × 24 SULFATE ION × 12 FE2/S2 (INORGANIC) CLUSTER × 3 FE (III) ION × 3 PHENYLETHANE × 3 water × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	NDOC_PSEU8
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–194； UniProt 1–194

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	4hm3
Deposition date deposition_date	2012-10-17
Structure title title	Naphthalene 1,2-Dioxygenase bound to ethylbenzene
Keywords keywords	Oxidoreductase-Oxidoreductase inhibitor complex; Oxidoreductase/Oxidoreductase inhibitor
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.

4hm3__assembly_1__model_1

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

Download this curve (.dat)

4hm3__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4hm3__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	36.32 Å
Rg (electron density)	35.30 Å
Total Rg	35.91 Å
Atom count	15414
Residues	1914
Excluded volume	271280 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4hm3__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 (8)

Entity 1 Entity 1 polymer

Description description	Naphthalene 1,2-dioxygenase subunit alpha
Molecular weight formula_weight	49664.4 kDa
EC 编号 ec_number	1.14.12.12
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	6067

MNYNNKILVSESGLSQKHLIHGDEELFQHELKTIFARNWLFLTHDSLIPAPGDYVTAKMGIDEVIVSRQNDGSIRAFLNVCRHRGKTLVSVEAGNAKGFVCSYHGWGFGSNGELQSVPFEKDLYGESLNKKCLGLKEVARVESFHGFIYGCFDQEAPPLMDYLGDAAWYLEPMFKHSGGLELVGPPGKVVIKANWKAPAENFVGDAYHVGWTHASSLRSGESIFSSLAGNAALPPEGAGLQMTSKYGSGMGVLWDGYSGVHSADLVPELMAFGGAKQERLNKEIGDVRARIYRSHLNCTVFPNNSMLTCSGVFKVWNPIDANTTEVWTYAIVEKDMPEDLKRRLADSVQRTFGPAGFWESDDNDNMETASQNGKKYQSRDSDLLSNLGFGEDVYGDAVYPGVVGKSAIGETSYRGFYRAYQAHVSSSNWAEFEHASSTWHTELTKTTDR

Source Source

Source organism organism	Pseudomonas sp. C18
NCBI taxonomy ID ncbi_taxonomy_id	69011
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Naphthalene 1,2-dioxygenase subunit beta
Molecular weight formula_weight	22969.1 kDa
EC 编号 ec_number	1.14.12.12
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

MMINIQEDKLVSAHDAEEILRFFNCHDSALQQEATTLLTQEAHLLDIQAYRAWLEHCVGSEVQYQVISRELRAASERRYKLNEAMNVYNENFQQLKVRVEHQLDPQNWGNSPKLRFTRFITNVQAAMDVNDKELLHIRSNVILHRARRGNQVDVFYAAREDKWKRGEGGVRKLVQRFVDYPERILQTHNLMVFL

Source Source

Source organism organism	Pseudomonas sp. C18
NCBI taxonomy ID ncbi_taxonomy_id	69011
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	8

Entity 4 Entity 4 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 5 Entity 5 non-polymer

Description description	FE2/S2 (INORGANIC) CLUSTER
Molecular weight formula_weight	175.8 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 non-polymer

Description description	FE (III) ION
Molecular weight formula_weight	55.8 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 7 Entity 7 non-polymer

Description description	PHENYLETHANE
Molecular weight formula_weight	106.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 8 Entity 8 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	901

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6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d4hm3a1
Class class	b — All beta proteins
Fold Fold fold	b.33 — ISP domain
Superfamily Superfamily superfamily	b.33.1 — ISP domain
Family Family family	b.33.1.2 — Ring hydroxylating alpha subunit ISP domain

Domain ID domain_id	d4hm3a2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.129 — TBP-like
Superfamily Superfamily superfamily	d.129.3 — Bet v1-like
Family Family family	d.129.3.3 — Ring hydroxylating alpha subunit catalytic domain

Domain ID domain_id	d4hm3b_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.17 — Cystatin-like
Superfamily Superfamily superfamily	d.17.4 — NTF2-like
Family Family family	d.17.4.4 — Ring hydroxylating beta subunit

CATH v4.4 (3 domains)

Domain ID domain_id	4hm3A01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	380 — Naphthalene 1,2-dioxygenase Alpha Subunit; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — Naphthalene 1,2-dioxygenase Alpha Subunit; Chain A, domain 1

Domain ID domain_id	4hm3A02
Class class	2 — Mainly Beta
Architecture architecture	102 — 3-layer Sandwich
Topology topology	10 — Rieske Iron-sulfur Protein
Homologous superfamily homologous superfamily	10 — Rieske [2Fe-2S] iron-sulphur domain

Domain ID domain_id	4hm3B00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	450 — Nuclear Transport Factor 2; Chain: A,
Homologous superfamily homologous superfamily	50 —

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Unit-cell length a length_a	139.940 Å
Unit-cell length b length_b	139.940 Å
Unit-cell length c length_c	208.253 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	18

Space group space_group	H 3 2
Space-group number int_tables_number	155
Crystal system crystal_system	—

Resolution resolution	1.500 Å
Low-resolution limit resolution_low	15.945 Å
R factor r_factor	0.1668
R_work r_work	0.1649
R_free r_free	0.2032

Naphthalene 1,2-Dioxygenase bound to ethylbenzene

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

Naphthalene 1,2-dioxygenase subunit alpha

State in the Current Structure

Other States of the Same Protein in the Database

Naphthalene 1,2-dioxygenase subunit beta

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

4hm3__assembly_1__model_1

4hm3__assembly_1__model_1 | I(q)

4hm3__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 (8)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 water

6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

CATH v4.4 (3 domains)

7. Citations (1)

Naphthalene 1,2-Dioxygenase bound to ethylbenzene

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

Naphthalene 1,2-dioxygenase subunit alpha

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Naphthalene 1,2-dioxygenase subunit beta

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

4hm3__assembly_1__model_1

4hm3__assembly_1__model_1 | I(q)

4hm3__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 (8)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 water

6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

CATH v4.4 (3 domains)

7. Citations (1)