1ar1

Structure at 2.7 Angstrom Resolution of the Paracoccus Denitrificans two-subunit Cytochrome C Oxidase Complexed with an Antibody Fv Fragment

Method: X-RAY DIFFRACTION D_max: 115.0 Å Quality: GOOD

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

CYTOCHROME C OXIDASE

Paracoccus denitrificans

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 heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 1–558	Not recorded	CYTOCHROME C OXIDASE × 1 （P08306） ANTIBODY FV FRAGMENT × 1 ANTIBODY FV FRAGMENT × 1 CU COPPER (II) ION × 3 MG MAGNESIUM ION × 1 CA CALCIUM ION × 1 HEA HEME-A × 2 LDA LAURYL DIMETHYLAMINE-N-OXIDE × 9	X-RAY DIFFRACTION X-ray crystallization conditions：pH 5.5；pH 5.5	Resolution 2.70 Å R-free 0.261

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 1AR1	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1QLE CRYO-STRUCTURE OF THE PARACOCCUS DENITRIFICANS FOUR-SUBUNIT CYTOCHROME C OXIDASE IN THE COMPLETELY OXIDIZED STATE COMPLEXED WITH AN ANTIBODY FV FRAGMENT Deposited 1999-08-30	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 17–554（538 aa）	Not recorded	HEA HEME-A × 2 CU COPPER (II) ION × 1 CA CALCIUM ION × 1 MN MANGANESE (II) ION × 1 CUA DINUCLEAR COPPER ION × 1 PC1 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 8；pH 8.00	Resolution 3.00 Å R-free 0.309
3EHB A D-Pathway Mutation Decouples the Paracoccus Denitrificans Cytochrome c Oxidase by Altering the side chain orientation of a distant, conserved Glutamate Deposited 2008-09-12	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–558（558 aa） Fragment：UNP residues 17-545	Mutation：N131D	HEA HEME-A × 2 CU COPPER (II) ION × 3 MG MAGNESIUM ION × 1 CA CALCIUM ION × 1 LDA LAURYL DIMETHYLAMINE-N-OXIDE × 9 LMT DODECYL-BETA-D-MALTOSIDE × 12 PER PEROXIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.3；291 K；MPEG 2000 is contained in the crystallization buffer pH 5.5, pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.32 Å R-free 0.242
3HB3 High resolution crystal structure of Paracoccus denitrificans cytochrome c oxidase Deposited 2009-05-04	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–558（558 aa）	Not recorded	HEA HEME-A × 2 CU1 COPPER (I) ION × 3 MN MANGANESE (II) ION × 1 CA CALCIUM ION × 1 LDA LAURYL DIMETHYLAMINE-N-OXIDE × 10 LMT DODECYL-BETA-D-MALTOSIDE × 14 PEO HYDROGEN PEROXIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 5.5；277 K；25% glycerol, pH 5.5, VAPOR DIFFUSION, temperature 277K	Resolution 2.25 Å R-free 0.280
7ATE Cytochrome c oxidase structure in P-state Deposited 2020-10-30	Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–558（558 aa）	Not recorded	MN MANGANESE (II) ION × 1 HEA HEME-A × 2 CU COPPER (II) ION × 1 CA CALCIUM ION × 1 PEO HYDROGEN PEROXIDE × 1 CUA DINUCLEAR COPPER ION × 1 PC1 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 1 PGV (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE；4 second before plunging	Resolution 2.40 Å
7ATN Cytochrome c oxidase structure in R-state Deposited 2020-10-30	Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–558（558 aa）	Not recorded	MN MANGANESE (II) ION × 1 HEA HEME-A × 2 CU COPPER (II) ION × 1 CA CALCIUM ION × 1 CUA DINUCLEAR COPPER ION × 1 PC1 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE；4 seconds before plunging	Resolution 2.66 Å
7AU3 Cytochrome c oxidase structure in F-state Deposited 2020-11-02	Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–558（558 aa）	Not recorded	MN MANGANESE (II) ION × 1 HEA HEME-A × 2 CU COPPER (II) ION × 1 CA CALCIUM ION × 1 O OXYGEN ATOM × 1 2FK SUPEROXO ION × 1 CUA DINUCLEAR COPPER ION × 1 PGV (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE；4 seconds before plunging	Resolution 2.56 Å
7AU6 Cytochrome c oxidase structure in O-state Deposited 2020-11-02	Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–558（558 aa）	Not recorded	HEA HEME-A × 2 CU COPPER (II) ION × 1 CA CALCIUM ION × 1 OXY OXYGEN MOLECULE × 6 PEO HYDROGEN PEROXIDE × 1 MN MANGANESE (II) ION × 1 CUA DINUCLEAR COPPER ION × 1 PC1 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE；4 seconds before plunging	Resolution 2.40 Å

7 other PDB entries and 7 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	CX1B_PARDE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–558； UniProt 1–558

CYTOCHROME C OXIDASE

Paracoccus denitrificans

UniProt P08306

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 heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain B； UniProt 1–298	Not recorded	CYTOCHROME C OXIDASE × 1 （P98002） ANTIBODY FV FRAGMENT × 1 ANTIBODY FV FRAGMENT × 1 CU COPPER (II) ION × 3 MG MAGNESIUM ION × 1 CA CALCIUM ION × 1 HEA HEME-A × 2 LDA LAURYL DIMETHYLAMINE-N-OXIDE × 9	X-RAY DIFFRACTION X-ray crystallization conditions：pH 5.5；pH 5.5	Resolution 2.70 Å R-free 0.261

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 1AR1	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1QLE CRYO-STRUCTURE OF THE PARACOCCUS DENITRIFICANS FOUR-SUBUNIT CYTOCHROME C OXIDASE IN THE COMPLETELY OXIDIZED STATE COMPLEXED WITH AN ANTIBODY FV FRAGMENT Deposited 1999-08-30	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain B 30–281（252 aa）	Not recorded	HEA HEME-A × 2 CU COPPER (II) ION × 1 CA CALCIUM ION × 1 MN MANGANESE (II) ION × 1 CUA DINUCLEAR COPPER ION × 1 PC1 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 8；pH 8.00	Resolution 3.00 Å R-free 0.309
3EHB A D-Pathway Mutation Decouples the Paracoccus Denitrificans Cytochrome c Oxidase by Altering the side chain orientation of a distant, conserved Glutamate Deposited 2008-09-12	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 1–298（298 aa）	Not recorded	HEA HEME-A × 2 CU COPPER (II) ION × 3 MG MAGNESIUM ION × 1 CA CALCIUM ION × 1 LDA LAURYL DIMETHYLAMINE-N-OXIDE × 9 LMT DODECYL-BETA-D-MALTOSIDE × 12 PER PEROXIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.3；291 K；MPEG 2000 is contained in the crystallization buffer pH 5.5, pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.32 Å R-free 0.242
3HB3 High resolution crystal structure of Paracoccus denitrificans cytochrome c oxidase Deposited 2009-05-04	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 1–298（298 aa）	Not recorded	HEA HEME-A × 2 CU1 COPPER (I) ION × 3 MN MANGANESE (II) ION × 1 CA CALCIUM ION × 1 LDA LAURYL DIMETHYLAMINE-N-OXIDE × 10 LMT DODECYL-BETA-D-MALTOSIDE × 14 PEO HYDROGEN PEROXIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 5.5；277 K；25% glycerol, pH 5.5, VAPOR DIFFUSION, temperature 277K	Resolution 2.25 Å R-free 0.280
7ATE Cytochrome c oxidase structure in P-state Deposited 2020-10-30	Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 1–298（298 aa）	Not recorded	MN MANGANESE (II) ION × 1 HEA HEME-A × 2 CU COPPER (II) ION × 1 CA CALCIUM ION × 1 PEO HYDROGEN PEROXIDE × 1 CUA DINUCLEAR COPPER ION × 1 PC1 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 1 PGV (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE；4 second before plunging	Resolution 2.40 Å
7ATN Cytochrome c oxidase structure in R-state Deposited 2020-10-30	Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 1–298（298 aa）	Not recorded	MN MANGANESE (II) ION × 1 HEA HEME-A × 2 CU COPPER (II) ION × 1 CA CALCIUM ION × 1 CUA DINUCLEAR COPPER ION × 1 PC1 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE；4 seconds before plunging	Resolution 2.66 Å
7AU3 Cytochrome c oxidase structure in F-state Deposited 2020-11-02	Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 1–298（298 aa）	Not recorded	MN MANGANESE (II) ION × 1 HEA HEME-A × 2 CU COPPER (II) ION × 1 CA CALCIUM ION × 1 O OXYGEN ATOM × 1 2FK SUPEROXO ION × 1 CUA DINUCLEAR COPPER ION × 1 PGV (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE；4 seconds before plunging	Resolution 2.56 Å
7AU6 Cytochrome c oxidase structure in O-state Deposited 2020-11-02	Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 1–298（298 aa）	Not recorded	HEA HEME-A × 2 CU COPPER (II) ION × 1 CA CALCIUM ION × 1 OXY OXYGEN MOLECULE × 6 PEO HYDROGEN PEROXIDE × 1 MN MANGANESE (II) ION × 1 CUA DINUCLEAR COPPER ION × 1 PC1 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE；4 seconds before plunging	Resolution 2.40 Å

7 other PDB entries and 7 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	COX2_PARDE
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–298； UniProt 1–298

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.

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	1ar1
Deposition date deposition_date	1997-08-08
Structure title title	Structure at 2.7 Angstrom Resolution of the Paracoccus Denitrificans two-subunit Cytochrome C Oxidase Complexed with an Antibody Fv Fragment
Keywords keywords	;COMPLEX (OXIDOREDUCTASE-ANTIBODY), ELECTRON TRANSPORT, TRANSMEMBRANE, CYTOCHROME OXIDASE, ANTIBODY COMPLEX, COMPLEX (OXIDOREDUCTASE-ANTIBODY) complex ;; COMPLEX (OXIDOREDUCTASE/ANTIBODY)
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	33.85 Å
Radius of gyration Rg (electron density) rg_electron	33.13 Å
Forward intensity I(0) i0	174128000.00
Molecular weight molecular_weight	116060.0 kDa
Excluded volume excluded_volume	148940 Å³
Envelope volume envelope_volume	170100 Å³
Hydration-shell volume shell_volume	43595 Å³
Envelope diameter envelope_diameter	123.7 Å
Shell Rg shell_rg	39.21 Å
Envelope Rg envelope_rg	33.61 Å
Shape Rg shape_rg	33.12 Å
Total Rg total_rg	33.64 Å
Total atoms total_atoms	8191
Residues n_residues	1007
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	115.0 Å
Rg (real space) rg_real	34.00 Å
Rg uncertainty (real space) rg_real_error	0.99 Å
I(0) (real space) i0_real	1.7410e+08
I(0) uncertainty (real space) i0_real_error	3.1070e+06
Rg (reciprocal space) rg_reciprocal	33.91 Å
I(0) (reciprocal space) i0_reciprocal	174100000.0000
Solution quality estimate total_estimate	0.8568
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	34.3 Å
Skewness Skewness skewness	0.490
Kurtosis Kurtosis kurtosis	-0.314
Angular range angular_range	— – 0.2350 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	40550000.0000
Real-space data points n_real_points	48
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.796; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.855; Smooth: 0.890

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (10)

Entity 1 Entity 1 polymer

Description description	CYTOCHROME C OXIDASE
Molecular weight formula_weight	62486.6 kDa
EC 编号 ec_number	1.9.3.1
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	8243

MADAAVHGHGDHHDTRGFFTRWFMSTNHKDIGILYLFTAGIVGLISVCFTVYMRMELQHPGVQYMCLEGARLIADASAECTPNGHLWNVMITYHGVLMMFFVVIPALFGGFGNYFMPLHIGAPDMAFPRLNNLSYWMYVCGVALGVASLLAPGGNDQMGSGVGWVLYPPLSTTEAGYSMDLAIFAVHVSGASSILGAINIITTFLNMRAPGMTLFKVPLFAWSVFITAWLILLSLPVLAGAITMLLMDRNFGTQFFDPAGGGDPVLYQHILWFFGHPEVYIIILPGFGIISHVISTFAKKPIFGYLPMVLAMAAIGILGFVVWAHHMYTAGMSLTQQAYFMLATMTIAVPTGIKVFSWIATMWGGSIEFKTPMLWAFGFLFLFTVGGVTGVVLSQAPLDRVYHDTYYVVAHFHYVMSLGAVFGIFAGVYYWIGKMSGRQYPEWAGQLHFWMMFIGSNLIFFPQHFLGRQGMPRRYIDYPVEFAYWNNISSIGAYISFASFLFFIGIVFYTLFAGKRVNVPNYWNEHADTLEWTLPSPPPEHTFETLPKREDWDRAHAH

来源 Source

来源生物 organism	Paracoccus denitrificans
NCBI Class编号 ncbi_taxonomy_id	266
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	CYTOCHROME C OXIDASE
Molecular weight formula_weight	32563.6 kDa
EC 编号 ec_number	1.9.3.1
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

MMAIATKRRGVAAVMSLGVATMTAVPALAQDVLGDLPVIGKPVNGGMNFQPASSPLAHDQQWLDHFVLYIITAVTIFVCLLLLICIVRFNRRANPVPARFTHNTPIEVIWTLVPVLILVAIGAFSLPILFRSQEMPNDPDLVIKAIGHQWYWSYEYPNDGVAFDALMLEKEALADAGYSEDEYLLATDNPVVVPVGKKVLVQVTATDVIHAWTIPAFAVKQDAVPGRIAQLWFSVDQEGVYFGQCSELCGINHAYMPIVVKAVSQEKYEAWLAGAKEEFAADASDYLPASPVKLASAE

来源 Source

来源生物 organism	Paracoccus denitrificans
NCBI Class编号 ncbi_taxonomy_id	266
宿主生物 host_organism	Escherichia coli

Entity 3 Entity 3 polymer

Description description	ANTIBODY FV FRAGMENT
Molecular weight formula_weight	14324.9 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

EVKLQESGGDLVQPGGSLKLSCAASGFTFSSYTMSWVRQTPEKRLEWVASINNGGGRTYYPDTVKGRFTISRDNAKNTLYLQMSSLKSEDTAMYYCVRHEYYYAMDYWGQGTTVTVSSAWRHPQFGG

来源 Source

来源生物 organism	Mus musculus
通用名 common_name	house mouse
NCBI Class编号 ncbi_taxonomy_id	10090
宿主生物 host_organism	Escherichia coli

Entity 4 Entity 4 polymer

Description description	ANTIBODY FV FRAGMENT
Molecular weight formula_weight	13260.8 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D

DIELTQTPVSLSASVGETVTITCRASENIYSYLAWYQQKQGKSPQFLVYNAKTLGEGVPSRFSGSGSGTQFSLKINSLLPEDFGSYYCQHHYGTPPLTFGGGTKLEIKREQKLISEEDLM

来源 Source

来源生物 organism	Mus musculus
通用名 common_name	house mouse
NCBI Class编号 ncbi_taxonomy_id	10090
宿主生物 host_organism	Escherichia coli

Entity 5 Entity 5 non-polymer

Description description	COPPER (II) ION
Molecular weight formula_weight	63.5 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 6 Entity 6 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 7 Entity 7 non-polymer

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

Entity 8 Entity 8 non-polymer

Description description	HEME-A
Molecular weight formula_weight	852.8 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 9 Entity 9 non-polymer

Description description	LAURYL DIMETHYLAMINE-N-OXIDE
Molecular weight formula_weight	229.4 kDa
Source method src_method	syn
Copy count entity_count	9

Entity 10 Entity 10 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	52

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7. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (5 domains)

Domain ID domain_id	d1ar1a_
Class class	f — Membrane and cell surface proteins and peptides
Fold Fold fold	f.24 — Cytochrome c oxidase subunit I-like
Superfamily Superfamily superfamily	f.24.1 — Cytochrome c oxidase subunit I-like
Family Family family	f.24.1.1 — Cytochrome c oxidase subunit I-like

Domain ID domain_id	d1ar1b1
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	d1ar1b2
Class class	f — Membrane and cell surface proteins and peptides
Fold Fold fold	f.17 — Transmembrane helix hairpin
Superfamily Superfamily superfamily	f.17.2 — Cytochrome c oxidase subunit II-like, transmembrane region
Family Family family	f.17.2.1 — Cytochrome c oxidase subunit II-like, transmembrane region

Domain ID domain_id	d1ar1c_
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.1 — V set domains (antibody variable domain-like)

Domain ID domain_id	d1ar1d_
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.1 — V set domains (antibody variable domain-like)

CATH v4.4 (5 domains)

Domain ID domain_id	1ar1A00
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	1ar1B01
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	1ar1B02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	287 — Helix Hairpins
Homologous superfamily homologous superfamily	90 —

Domain ID domain_id	1ar1C00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	1ar1D00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

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8. Citations (1)

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Unit-cell length a length_a	93.500 Å
Unit-cell length b length_b	151.000 Å
Unit-cell length c length_c	156.700 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	2.700 Å
Low-resolution limit resolution_low	30.000 Å
R factor r_factor	0.2070
R_work r_work	0.2070
R_free r_free	0.2610

fit	/app/data/saxs_computation/ar/1ar1/1ar1.fit
pddf	/app/data/pr_computation/ar/1ar1/1ar1.pr.out
profile	/app/data/saxs_computation/ar/1ar1/1ar1.dat

Structure at 2.7 Angstrom Resolution of the Paracoccus Denitrificans two-subunit Cytochrome C Oxidase Complexed with an Antibody Fv Fragment

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

CYTOCHROME C OXIDASE

State in the Current Structure

Other States of the Same Protein in the Database

CYTOCHROME C OXIDASE

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

6. Entities and Polymers Entities & Polymers (10)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 polymer

Polymer Polymer

来源 Source

Entity 4 Entity 4 polymer

Polymer Polymer

来源 Source

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 water

7. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (5 domains)

CATH v4.4 (5 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)