5gux

Cytochrome c-dependent nitric oxide reductase (cNOR) from Pseudomonas aeruginosa in complex with xenon

Method: X-RAY DIFFRACTION

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

Nitric oxide reductase subunit B

OrganismNot specified

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
2	Protein heterocomplex	Heteromer	Protein 2	Nitric oxide reductase subunit C × 1 （Q59646） PROTOPORPHYRIN IX CONTAINING FE × 2 FE (III) ION × 1 OXYGEN ATOM × 1 XENON × 7 decyl 4-O-alpha-D-glucopyranosyl-1-thio-beta-D-glucopyranoside × 2 CALCIUM ION × 1 HEME C × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	NORB_PSEAE
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain B； PDBConstruct 1–465； UniProt 1–466

Nitric oxide reductase subunit C

OrganismNot specified

UniProt Q59646

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
2	Protein heterocomplex	Heteromer	Protein 2	Nitric oxide reductase subunit B × 1 （Q59647） PROTOPORPHYRIN IX CONTAINING FE × 2 FE (III) ION × 1 OXYGEN ATOM × 1 XENON × 7 decyl 4-O-alpha-D-glucopyranosyl-1-thio-beta-D-glucopyranoside × 2 CALCIUM ION × 1 HEME C × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	NORC_PSEAE
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain C； PDBConstruct 1–146； UniProt 1–146

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	5gux
Deposition date deposition_date	2016-08-31
Structure title title	Cytochrome c-dependent nitric oxide reductase (cNOR) from Pseudomonas aeruginosa in complex with xenon
Keywords keywords	metal-binding, membrane protein; MEMBRANE PROTEIN
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.

5gux__assembly_1__model_1

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

Download this curve (.dat)

5gux__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5gux__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	25.80 Å
Rg (electron density)	24.82 Å
Total Rg	25.64 Å
Atom count	3361
Residues	438
Excluded volume	59427 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5gux__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`5gux__assembly_2__model_1`	dimeric （2）	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 (11)

Entity 1 Entity 1 polymer

Description description	Antibody fab fragment light chain
Molecular weight formula_weight	23735.3 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	L
Atom count atom_count	8265

DIQMTQSPPYLAASPGETITINCRASKSIRKYLAWYQEKPGKTNKLLIYSGSTLQFGIPSRFSGSGSGTEFTLTISSLEPEDFAMYYCQQHNEYPLTFGAGTKLELKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNE

Entity 2 Entity 2 polymer

Description description	Antibody fab fragment heavy chain
Molecular weight formula_weight	24089.9 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	H

EVQLQQSGTVLARPGASVKMSCKASGYSFTSYWMHWVKQRPGQGLEWIGAVYPGNSDTSYNQKFKGKAKLTAVTSASTAYMELSSLTNEDSAVYYCSRSSLDGYYVKNWCFDVWGQGTTVTVSSAKTTAPSVYPLAPVCGDTTGSSVTLGCLVKGYFPEPVTLTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVTSSTRPSQSITCNVAHPASSTKVDKKIEPRG

Entity 3 Entity 3 polymer

Description description	Nitric oxide reductase subunit B
Molecular weight formula_weight	52215.9 kDa
EC 编号 ec_number	1.7.2.5
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

MMSPNGSLKFASQAVAKPYFVFALILFVGQILFGLIMGLQYVVGDFLFPAIPFNVARMVHTNLLIVWLLFGFMGAAYYLVPEESDCELYSPKLAWILFWVFAAAGVLTILGYLLVPYAGLARLTGNELWPTMGREFLEQPTISKAGIVIVALGFLFNVGMTVLRGRKTAISMVLMTGLIGLALLFLFSFYNPENLTRDKFYWWWVVHLWVEGVWELIMGAILAFVLVKITGVDREVIEKWLYVIIAMALISGIIGTGHHYFWIGVPGYWLWLGSVFSALEPLPFFAMVLFAFNTINRRRRDYPNRAVALWAMGTTVMAFLGAGVWGFMHTLAPVNYYTHGTQLTAAHGHMAFYGAYAMIVMTIISYAMPRLRGIGEAMDNRSQVLEMWGFWLMTVAMVFITLFLSAAGVLQVWLQRMPADGAAMTFMATQDQLAIFYWLREGAGVVFLIGLVAYLLSFRRGKAAA

Entity 4 Entity 4 polymer

Description description	Nitric oxide reductase subunit C
Molecular weight formula_weight	16374.6 kDa
Mutation mutation	K100N
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

MSETFTKGMARNIYFGGSVFFILLFLALTYHTEKTLPERTNEAAMSAAVVRGKLVWEQNNCVGCHTLLGEGAYFAPELGNVVGRRGGEEGFNTFLQAWMKIQPLNVPGRRAMPQFHLSEGQVDDLAEFLKWSSKIDTNQWPPNKEG

Entity 5 Entity 5 non-polymer

Description description	PROTOPORPHYRIN IX CONTAINING FE
Molecular weight formula_weight	616.5 kDa
Source method src_method	syn
Copy count entity_count	2

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	OXYGEN ATOM
Molecular weight formula_weight	16.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 8 Entity 8 non-polymer

Description description	XENON
Molecular weight formula_weight	131.3 kDa
Source method src_method	syn
Copy count entity_count	7

Entity 9 Entity 9 non-polymer

Description description	decyl 4-O-alpha-D-glucopyranosyl-1-thio-beta-D-glucopyranoside
Molecular weight formula_weight	498.6 kDa
Source method src_method	man
Copy count entity_count	2

Entity 10 Entity 10 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 11 Entity 11 non-polymer

Description description	HEME C
Molecular weight formula_weight	618.5 kDa
Source method src_method	syn
Copy count entity_count	1

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6. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

Domain ID domain_id	5guxB00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	210 — Cytochrome C Oxidase; Chain A
Homologous superfamily homologous superfamily	10 — Cytochrome c oxidase-like, subunit I domain

Domain ID domain_id	5guxC00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	760 — Cytochrome Bc1 Complex; Chain D, domain 2
Homologous superfamily homologous superfamily	10 — Cytochrome c-like domain

Domain ID domain_id	5guxH01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	5guxH02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	5guxL01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	5guxL02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

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Unit-cell length a length_a	89.843 Å
Unit-cell length b length_b	105.379 Å
Unit-cell length c length_c	192.577 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	4

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

Resolution resolution	3.300 Å
Low-resolution limit resolution_low	39.390 Å
R factor r_factor	0.2121
R_work r_work	0.2092
R_free r_free	0.2675

Cytochrome c-dependent nitric oxide reductase (cNOR) from Pseudomonas aeruginosa in complex with xenon

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

Nitric oxide reductase subunit B

State in the Current Structure

Other States of the Same Protein in the Database

Nitric oxide reductase subunit C

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

5gux__assembly_1__model_1

5gux__assembly_1__model_1 | I(q)

5gux__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 (11)

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 polymer

Polymer Polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 non-polymer

Entity 9 Entity 9 non-polymer

Entity 10 Entity 10 non-polymer

Entity 11 Entity 11 non-polymer

6. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

7. Citations (4)

Cytochrome c-dependent nitric oxide reductase (cNOR) from Pseudomonas aeruginosa in complex with xenon

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

Nitric oxide reductase subunit B

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Nitric oxide reductase subunit C

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

5gux__assembly_1__model_1

5gux__assembly_1__model_1 | I(q)

5gux__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 (11)

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 polymer

Polymer Polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 non-polymer

Entity 9 Entity 9 non-polymer

Entity 10 Entity 10 non-polymer

Entity 11 Entity 11 non-polymer

6. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

7. Citations (4)