5u7n

CRYSTAL STRUCTURE OF A CHIMERIC CUA DOMAIN (SUBUNIT II) OF CYTOCHROME BA3 FROM THERMUS THERMOPHILUS WITH THE AMICYANIN LOOP

Method: X-RAY DIFFRACTION

▼

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

Cytochrome c oxidase subunit 2

Thermus thermophilus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	COPPER (II) ION × 1 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	COPPER (II) ION × 1 water × 1	Consistent with protein count
3	Protein monomer	Monomer	Protein 1	COPPER (II) ION × 1 (4S)-2-METHYL-2,4-PENTANEDIOL × 1 water × 1	Consistent with protein count
4	Protein monomer	Monomer	Protein 1	COPPER (II) ION × 1 water × 1	Consistent with protein count
5	Protein monomer	Monomer	Protein 1	COPPER (II) ION × 1 water × 1	Consistent with protein count
6	Protein monomer	Monomer	Protein 1	COPPER (II) ION × 1 (4S)-2-METHYL-2,4-PENTANEDIOL × 1 water × 1	Consistent with protein count
7	Protein monomer	Monomer	Protein 1	COPPER (II) ION × 1 water × 1	Consistent with protein count
8	Protein monomer	Monomer	Protein 1	COPPER (II) ION × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	COX2_THETH
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 5–110； UniProt 11–116 Author chain A； PDBConstruct 116–124； UniProt 127–135 Author chain B； PDBConstruct 5–110； UniProt 11–116 Author chain B； PDBConstruct 116–124； UniProt 127–135 Author chain C； PDBConstruct 5–110； UniProt 11–116 Author chain C； PDBConstruct 116–124； UniProt 127–135 Author chain D； PDBConstruct 5–110； UniProt 11–116 Author chain D； PDBConstruct 116–124； UniProt 127–135 Author chain E； PDBConstruct 5–110； UniProt 11–116 Author chain E； PDBConstruct 116–124； UniProt 127–135 Author chain F； PDBConstruct 5–110； UniProt 11–116 Author chain F； PDBConstruct 116–124； UniProt 127–135 Author chain G； PDBConstruct 5–110； UniProt 11–116 Author chain G； PDBConstruct 116–124； UniProt 127–135 Author chain H； PDBConstruct 5–110； UniProt 11–116 Author chain H； PDBConstruct 116–124； UniProt 127–135

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	5u7n
Deposition date deposition_date	2016-12-12
Structure title title	CRYSTAL STRUCTURE OF A CHIMERIC CUA DOMAIN (SUBUNIT II) OF CYTOCHROME BA3 FROM THERMUS THERMOPHILUS WITH THE AMICYANIN LOOP
Keywords keywords	OXIDOREDUCTASE, ELECTRON TRANSPORT; OXIDOREDUCTASE
Experimental Method method	X-RAY DIFFRACTION

▼

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.

5u7n__assembly_1__model_1

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

Download this curve (.dat)

5u7n__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5u7n__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	14.86 Å
Rg (electron density)	13.46 Å
Total Rg	14.73 Å
Atom count	911
Residues	115
Excluded volume	16301 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5u7n__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`5u7n__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`5u7n__assembly_3__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`5u7n__assembly_4__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
5	1	`5u7n__assembly_5__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
6	1	`5u7n__assembly_6__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
7	1	`5u7n__assembly_7__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
8	1	`5u7n__assembly_8__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Cytochrome c oxidase subunit 2
Molecular weight formula_weight	13706.6 kDa
EC 编号 ec_number	1.9.3.1,1.9.3.1
Source method src_method	man
Copy count entity_count	8

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G,H
Atom count atom_count	7729

GSHMVIPAGKLERVDPTTVRQEGPWADPAQAVVQTGPNQYTVYVLAFAFGYQPNPIEVPQGAEIVFKITSPDVIHGFHVEGTNINVEVLPGEVSTVRYTFKRPGEYRIICTPHPFMFGTIVVKE

Source Source

Source organism organism	Thermus thermophilus
NCBI taxonomy ID ncbi_taxonomy_id	274
Host organism host_organism	Escherichia coli BL21

Entity 2 Entity 2 non-polymer

Description description	COPPER (II) ION
Molecular weight formula_weight	63.5 kDa
Source method src_method	syn
Copy count entity_count	8

Entity 3 Entity 3 non-polymer

Description description	(4S)-2-METHYL-2,4-PENTANEDIOL
Molecular weight formula_weight	118.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	541

▼

6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

Domain ID domain_id	d5u7na_
Class class	b — All beta proteins
Fold Fold fold	b.6 — Cupredoxin-like
Superfamily Superfamily superfamily	b.6.1 — Cupredoxins
Family Family family	b.6.1.2 — Periplasmic domain of cytochrome c oxidase subunit II

Domain ID domain_id	d5u7nb_
Class class	b — All beta proteins
Fold Fold fold	b.6 — Cupredoxin-like
Superfamily Superfamily superfamily	b.6.1 — Cupredoxins
Family Family family	b.6.1.2 — Periplasmic domain of cytochrome c oxidase subunit II

Domain ID domain_id	d5u7nc_
Class class	b — All beta proteins
Fold Fold fold	b.6 — Cupredoxin-like
Superfamily Superfamily superfamily	b.6.1 — Cupredoxins
Family Family family	b.6.1.2 — Periplasmic domain of cytochrome c oxidase subunit II

Domain ID domain_id	d5u7nd_
Class class	b — All beta proteins
Fold Fold fold	b.6 — Cupredoxin-like
Superfamily Superfamily superfamily	b.6.1 — Cupredoxins
Family Family family	b.6.1.2 — Periplasmic domain of cytochrome c oxidase subunit II

Domain ID domain_id	d5u7ne_
Class class	b — All beta proteins
Fold Fold fold	b.6 — Cupredoxin-like
Superfamily Superfamily superfamily	b.6.1 — Cupredoxins
Family Family family	b.6.1.2 — Periplasmic domain of cytochrome c oxidase subunit II

Domain ID domain_id	d5u7nf_
Class class	b — All beta proteins
Fold Fold fold	b.6 — Cupredoxin-like
Superfamily Superfamily superfamily	b.6.1 — Cupredoxins
Family Family family	b.6.1.2 — Periplasmic domain of cytochrome c oxidase subunit II

Domain ID domain_id	d5u7ng_
Class class	b — All beta proteins
Fold Fold fold	b.6 — Cupredoxin-like
Superfamily Superfamily superfamily	b.6.1 — Cupredoxins
Family Family family	b.6.1.2 — Periplasmic domain of cytochrome c oxidase subunit II

Domain ID domain_id	d5u7nh_
Class class	b — All beta proteins
Fold Fold fold	b.6 — Cupredoxin-like
Superfamily Superfamily superfamily	b.6.1 — Cupredoxins
Family Family family	b.6.1.2 — Periplasmic domain of cytochrome c oxidase subunit II

CATH v4.4 (8 domains)

Domain ID domain_id	5u7nA00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	420 — Cupredoxins - blue copper proteins

Domain ID domain_id	5u7nB00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	420 — Cupredoxins - blue copper proteins

Domain ID domain_id	5u7nC00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	420 — Cupredoxins - blue copper proteins

Domain ID domain_id	5u7nD00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	420 — Cupredoxins - blue copper proteins

Domain ID domain_id	5u7nE00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	420 — Cupredoxins - blue copper proteins

Domain ID domain_id	5u7nF00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	420 — Cupredoxins - blue copper proteins

Domain ID domain_id	5u7nG00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	420 — Cupredoxins - blue copper proteins

Domain ID domain_id	5u7nH00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	420 — Cupredoxins - blue copper proteins

▶

Unit-cell length a length_a	94.352 Å
Unit-cell length b length_b	100.701 Å
Unit-cell length c length_c	101.103 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	32

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

Resolution resolution	2.300 Å
Low-resolution limit resolution_low	45.180 Å
R factor r_factor	0.1783
R_work r_work	0.1759
R_free r_free	0.2258

CRYSTAL STRUCTURE OF A CHIMERIC CUA DOMAIN (SUBUNIT II) OF CYTOCHROME BA3 FROM THERMUS THERMOPHILUS WITH THE AMICYANIN LOOP

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

Cytochrome c oxidase 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

5u7n__assembly_1__model_1

5u7n__assembly_1__model_1 | I(q)

5u7n__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

CATH v4.4 (8 domains)

7. Citations (1)

CRYSTAL STRUCTURE OF A CHIMERIC CUA DOMAIN (SUBUNIT II) OF CYTOCHROME BA3 FROM THERMUS THERMOPHILUS WITH THE AMICYANIN LOOP

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

Cytochrome c oxidase 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

5u7n__assembly_1__model_1

5u7n__assembly_1__model_1 | I(q)

5u7n__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

CATH v4.4 (8 domains)

7. Citations (1)