SAXSdb — 2yj5

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

COPPER-TRANSPORTING ATPASE

SULFOLOBUS SOLFATARICUS

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	5'-O-[(S)-hydroxy{[(R)-hydroxy({(S)-hydroxy[(1S)-1-(2-nitrophenyl)ethoxy]phosphoryl}oxy)phosphoryl]oxy}phosphoryl]adenosine × 1 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	ADENOSINE-5'-TRIPHOSPHATE × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q97UU7_SULSO
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–263； UniProt 383–645 Author chain B； PDBConstruct 1–263； UniProt 383–645

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	2yj5
Deposition date deposition_date	2011-05-18
Structure title title	Conformational changes in the catalytic domain of the CPx-ATPase CopB- B upon nucleotide binding
Keywords keywords	HYDROLASE, P-TYPE ATPASE, COPB, HEAVY METAL TRANSLOCATION; HYDROLASE
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.

2yj5__assembly_2__model_1

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

Download this curve (.dat)

2yj5__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2yj5__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	20.76 Å
Rg (electron density)	20.25 Å
Total Rg	21.10 Å
Atom count	1933
Residues	252
Excluded volume	34952 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2yj5__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2yj5__assembly_2__model_1`	monomeric （1）	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 (4)

Entity 1 Entity 1 polymer

Description description	COPPER-TRANSPORTING ATPASE
Molecular weight formula_weight	28825.4 kDa
EC 编号 ec_number	3.6.1.36, 3.6.3.10
Mutation mutation	YES
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	3808

MALSLYEKMLHKGMIIKNSNVYEKIKEIDTIIFNKTGTLTYGTPIVTQFIGDSLSLAYAASVEALSSHPIAKAIVKYAKEQGVKILEVKDFKEISGIGVRGKISDKIIEVKKAENNNDIAVYINGEPIASFNISDVPRPNLKDYLEKLKNEGLKIIILSGDKEDKVKELSKELNIQEYYSNLSPEDKVRIIEKLKQNGNKVLMIGDGVNDAAALALADVSVAMGNGVDISKNVADIILVSNDIGTLLGLIKNRKRLSNAIPSN

Source Source

Source organism organism	SULFOLOBUS SOLFATARICUS
NCBI taxonomy ID ncbi_taxonomy_id	273057
Host organism host_organism	ESCHERICHIA COLI

Entity 2 Entity 2 non-polymer

Description description	5'-O-[(S)-hydroxy{[(R)-hydroxy({(S)-hydroxy[(1S)-1-(2-nitrophenyl)ethoxy]phosphoryl}oxy)phosphoryl]oxy}phosphoryl]adenosine
Molecular weight formula_weight	656.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	ADENOSINE-5'-TRIPHOSPHATE
Molecular weight formula_weight	507.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	41

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6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	2yj5A01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1000 — HAD superfamily/HAD-like

Domain ID domain_id	2yj5A02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1110 — Calcium-transporting ATPase, cytoplasmic domain N
Homologous superfamily homologous superfamily	10 — Calcium-transporting ATPase, cytoplasmic domain N

Domain ID domain_id	2yj5B01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1000 — HAD superfamily/HAD-like

Domain ID domain_id	2yj5B02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1110 — Calcium-transporting ATPase, cytoplasmic domain N
Homologous superfamily homologous superfamily	10 — Calcium-transporting ATPase, cytoplasmic domain N

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Unit-cell length a length_a	54.020 Å
Unit-cell length b length_b	76.180 Å
Unit-cell length c length_c	137.640 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	8

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

Resolution resolution	2.400 Å
Low-resolution limit resolution_low	44.065 Å
R factor r_factor	0.2397
R_work r_work	0.2371
R_free r_free	0.2864

Conformational changes in the catalytic domain of the CPx-ATPase CopB- B upon nucleotide binding

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

COPPER-TRANSPORTING ATPASE

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

2yj5__assembly_2__model_1

2yj5__assembly_2__model_1 | I(q)

2yj5__assembly_2__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 (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) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)

Conformational changes in the catalytic domain of the CPx-ATPase CopB- B upon nucleotide binding

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

COPPER-TRANSPORTING ATPASE

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

2yj5__assembly_2__model_1

2yj5__assembly_2__model_1 | I(q)

2yj5__assembly_2__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 (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) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)