SAXSdb — 6pty

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

Cytochrome c oxidase subunit 2

Thermus thermophilus

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 11–135	Not recorded	CUA DINUCLEAR COPPER ION × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；291 K；100 mM Hepes, 1.6 M (NH4)2SO4, 0.1 mM NaCl, pH 7.5	Resolution 1.98 Å R-free 0.238
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 11–135	Not recorded	CUA DINUCLEAR COPPER ION × 1 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；291 K；100 mM Hepes, 1.6 M (NH4)2SO4, 0.1 mM NaCl, pH 7.5	Resolution 1.98 Å R-free 0.238

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 6PTY	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1XME Structure of Recombinant Cytochrome ba3 Oxidase from Thermus thermophilus Deposited 2004-10-01	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 1–168（168 aa）	Not recorded	BNG nonyl beta-D-glucopyranoside × 1 CU COPPER (II) ION × 1 HEM PROTOPORPHYRIN IX CONTAINING FE × 1 HAS HEME-AS × 1 GOL GLYCEROL × 1 CUA DINUCLEAR COPPER ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；297 K；Peg 2000, Bis-tris, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 297K	Resolution 2.30 Å R-free 0.236
2CUA THE CUA DOMAIN OF CYTOCHROME BA3 FROM THERMUS THERMOPHILUS Deposited 1999-02-18	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 34–168（135 aa） Fragment：SOLUBLE CUA-CONTAINING DOMAIN	Not recorded	ZN ZINC ION × 1 CUA DINUCLEAR COPPER ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；0.2-20% MPEG 5K 100MM NA CACODYLATE PH 6.5 1MM ZNCL2	Resolution 1.60 Å R-free 0.296
2CUA THE CUA DOMAIN OF CYTOCHROME BA3 FROM THERMUS THERMOPHILUS Deposited 1999-02-18	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 34–168（135 aa） Fragment：SOLUBLE CUA-CONTAINING DOMAIN	Not recorded	ZN ZINC ION × 1 CUA DINUCLEAR COPPER ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；0.2-20% MPEG 5K 100MM NA CACODYLATE PH 6.5 1MM ZNCL2	Resolution 1.60 Å R-free 0.296
2FWL The cytochrome c552/CuA complex from Thermus thermophilus Deposited 2006-02-02	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–135（135 aa）	Not recorded	HEC HEME C × 1 CUA DINUCLEAR COPPER ION × 1	SOLUTION NMR NMR measurement conditions pH 6；298 K；Ionic strength (raw mmCIF value) 20mM phosphate buffer；Pressure ambient NMR sample composition 0.5mM cytochrome c552 U-15N, 20mM phosphate buffer, 2mM CuA domain, 95% H2O, 5% D2O \| 95% H2O/5% D2O NMR sample composition 0.5mM CuA domain U-15N, 20mM phosphate buffer, 2mM cytochrome c552, 95% H2O, 5% D2O \| 95% H2O/5% D2O	Resolution not provided
2LLN Solution structure of Thermus thermophilus apo-CuA Deposited 2011-11-15	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 11–135（125 aa） Fragment：UNP residues 11-135	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6；298 K；Ionic strength (raw mmCIF value) 0.1；Pressure ambient NMR sample composition 0.8 -1 mM [U-99% 13C; U-99% 15N] protein, 100 mM potassium phosphate, 2 mM DTT, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 0.8 -1 mM [U-99% 15N] protein, 100 mM potassium phosphate, 2 mM DTT, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 0.8 - 1 mM protein, 100 mM potassium phosphate, 2 mM DTT, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
5U7N CRYSTAL STRUCTURE OF A CHIMERIC CUA DOMAIN (SUBUNIT II) OF CYTOCHROME BA3 FROM THERMUS THERMOPHILUS WITH THE AMICYANIN LOOP Deposited 2016-12-12	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 11–116（106 aa） Fragment：UNP residues 11-116,127-135 Chain A 127–135（9 aa） Fragment：UNP residues 11-116,127-135	Not recorded	CU COPPER (II) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；295 K；60 % (4S)-2-METHYL-2,4-PENTANEDIOL	Resolution 2.30 Å R-free 0.226
5U7N CRYSTAL STRUCTURE OF A CHIMERIC CUA DOMAIN (SUBUNIT II) OF CYTOCHROME BA3 FROM THERMUS THERMOPHILUS WITH THE AMICYANIN LOOP Deposited 2016-12-12	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 11–116（106 aa） Fragment：UNP residues 11-116,127-135 Chain B 127–135（9 aa） Fragment：UNP residues 11-116,127-135	Not recorded	CU COPPER (II) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；295 K；60 % (4S)-2-METHYL-2,4-PENTANEDIOL	Resolution 2.30 Å R-free 0.226
5U7N CRYSTAL STRUCTURE OF A CHIMERIC CUA DOMAIN (SUBUNIT II) OF CYTOCHROME BA3 FROM THERMUS THERMOPHILUS WITH THE AMICYANIN LOOP Deposited 2016-12-12	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 11–116（106 aa） Fragment：UNP residues 11-116,127-135 Chain C 127–135（9 aa） Fragment：UNP residues 11-116,127-135	Not recorded	CU COPPER (II) ION × 1 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；295 K；60 % (4S)-2-METHYL-2,4-PENTANEDIOL	Resolution 2.30 Å R-free 0.226
5U7N CRYSTAL STRUCTURE OF A CHIMERIC CUA DOMAIN (SUBUNIT II) OF CYTOCHROME BA3 FROM THERMUS THERMOPHILUS WITH THE AMICYANIN LOOP Deposited 2016-12-12	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain D 11–116（106 aa） Fragment：UNP residues 11-116,127-135 Chain D 127–135（9 aa） Fragment：UNP residues 11-116,127-135	Not recorded	CU COPPER (II) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；295 K；60 % (4S)-2-METHYL-2,4-PENTANEDIOL	Resolution 2.30 Å R-free 0.226
5U7N CRYSTAL STRUCTURE OF A CHIMERIC CUA DOMAIN (SUBUNIT II) OF CYTOCHROME BA3 FROM THERMUS THERMOPHILUS WITH THE AMICYANIN LOOP Deposited 2016-12-12	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 5 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain E 11–116（106 aa） Fragment：UNP residues 11-116,127-135 Chain E 127–135（9 aa） Fragment：UNP residues 11-116,127-135	Not recorded	CU COPPER (II) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；295 K；60 % (4S)-2-METHYL-2,4-PENTANEDIOL	Resolution 2.30 Å R-free 0.226
5U7N CRYSTAL STRUCTURE OF A CHIMERIC CUA DOMAIN (SUBUNIT II) OF CYTOCHROME BA3 FROM THERMUS THERMOPHILUS WITH THE AMICYANIN LOOP Deposited 2016-12-12	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 6 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain F 11–116（106 aa） Fragment：UNP residues 11-116,127-135 Chain F 127–135（9 aa） Fragment：UNP residues 11-116,127-135	Not recorded	CU COPPER (II) ION × 1 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；295 K；60 % (4S)-2-METHYL-2,4-PENTANEDIOL	Resolution 2.30 Å R-free 0.226
5U7N CRYSTAL STRUCTURE OF A CHIMERIC CUA DOMAIN (SUBUNIT II) OF CYTOCHROME BA3 FROM THERMUS THERMOPHILUS WITH THE AMICYANIN LOOP Deposited 2016-12-12	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 7 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain G 11–116（106 aa） Fragment：UNP residues 11-116,127-135 Chain G 127–135（9 aa） Fragment：UNP residues 11-116,127-135	Not recorded	CU COPPER (II) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；295 K；60 % (4S)-2-METHYL-2,4-PENTANEDIOL	Resolution 2.30 Å R-free 0.226
5U7N CRYSTAL STRUCTURE OF A CHIMERIC CUA DOMAIN (SUBUNIT II) OF CYTOCHROME BA3 FROM THERMUS THERMOPHILUS WITH THE AMICYANIN LOOP Deposited 2016-12-12	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 8 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain H 11–116（106 aa） Fragment：UNP residues 11-116,127-135 Chain H 127–135（9 aa） Fragment：UNP residues 11-116,127-135	Not recorded	CU COPPER (II) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；295 K；60 % (4S)-2-METHYL-2,4-PENTANEDIOL	Resolution 2.30 Å R-free 0.226
6PTT Soluble model of Arabidopsis thaliana CuA (Tt3LAt) Deposited 2019-07-16	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 11–135（125 aa）	Not recorded	CUA DINUCLEAR COPPER ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；291 K；100 mM Hepes, 1.5 M LiSO4, pH 7.5	Resolution 1.84 Å R-free 0.214
6PTT Soluble model of Arabidopsis thaliana CuA (Tt3LAt) Deposited 2019-07-16	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 11–135（125 aa）	Not recorded	CUA DINUCLEAR COPPER ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；291 K；100 mM Hepes, 1.5 M LiSO4, pH 7.5	Resolution 1.84 Å R-free 0.214

6 other PDB entries and 15 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	COX2_THETH
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 5–129； UniProt 11–135 Author chain B； PDBConstruct 5–129； UniProt 11–135

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	6pty
Deposition date deposition_date	2019-07-16
Structure title title	Soluble model of human CuA (Tt3Lh)
Keywords keywords	CuA site, electron transfer, cupredoxin fold, ELECTRON TRANSPORT, OXIDOREDUCTASE; ELECTRON TRANSPORT, OXIDOREDUCTASE
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	21.56 Å
Radius of gyration Rg (electron density) rg_electron	21.35 Å
Forward intensity I(0) i0	13569800.00
Molecular weight molecular_weight	27142.0 kDa
Excluded volume excluded_volume	33703 Å³
Envelope volume envelope_volume	39535 Å³
Hydration-shell volume shell_volume	16864 Å³
Envelope diameter envelope_diameter	84.4 Å
Shell Rg shell_rg	26.14 Å
Envelope Rg envelope_rg	21.80 Å
Shape Rg shape_rg	21.40 Å
Total Rg total_rg	21.89 Å
Total atoms total_atoms	1903
Residues n_residues	238
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	82.4 Å
Rg (real space) rg_real	21.81 Å
Rg uncertainty (real space) rg_real_error	0.77 Å
I(0) (real space) i0_real	1.3570e+07
I(0) uncertainty (real space) i0_real_error	2.0600e+05
Rg (reciprocal space) rg_reciprocal	21.76 Å
I(0) (reciprocal space) i0_reciprocal	13570000.0000
Solution quality estimate total_estimate	0.7629
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	21.8 Å
Skewness Skewness skewness	0.652
Kurtosis Kurtosis kurtosis	0.065
Angular range angular_range	— – 0.3700 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	2161000.0000
Real-space data points n_real_points	69
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.474; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.493; Smooth: 0.998

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	Cytochrome c oxidase subunit 2
Molecular weight formula_weight	14364.2 kDa
EC 编号 ec_number	1.9.3.1
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	2138

GSHMVIPAGKLERVDPTTVRQEGPWADPAQAVVQTGPNQYTVYVLAHQWYYQPNPIEVPQGAEIVFKITSQDVLHGFHVEGTNINVEVLPGEVSTVRYTFKRPGEYRIICSEICGANHSNMFGTIVVKE

来源 Source

来源生物 organism	Thermus thermophilus
NCBI Class编号 ncbi_taxonomy_id	274
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	DINUCLEAR COPPER ION
Molecular weight formula_weight	127.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	1

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	1

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	229

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d6ptya_
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	d6ptyb_
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 (2 domains)

Domain ID domain_id	6ptyA00
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	6ptyB00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	420 — Cupredoxins - blue copper proteins

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8. Citations (1)

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Unit-cell length a length_a	51.630 Å
Unit-cell length b length_b	70.957 Å
Unit-cell length c length_c	77.415 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	orthorhombic

Resolution resolution	1.980 Å
Low-resolution limit resolution_low	42.950 Å
R factor r_factor	0.2002
R_work r_work	0.1982
R_free r_free	0.2383

fit	/app/data/saxs_computation/pt/6pty/6pty.fit
pddf	/app/data/pr_computation/pt/6pty/6pty.pr.out
profile	/app/data/saxs_computation/pt/6pty/6pty.dat

Soluble model of human CuA (Tt3Lh)

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

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction