2ciy

Chloroperoxidase complexed with cyanide and DMSO

Method: X-RAY DIFFRACTION D_max: 60.6 Å Quality: REASONABLE

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

CHLOROPEROXIDASE

OrganismNot specified

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Other combination Monomer Protein × 1 其他Polymer 3 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 21–319	Fragment：RESIDUES 21-319 Non-standard monomer：Yes (specific site not provided by mmCIF)	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 2 alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose × 1 MN MANGANESE (II) ION × 1 HEM PROTOPORPHYRIN IX CONTAINING FE × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 MAN alpha-D-mannopyranose × 11 BR BROMIDE ION × 2 EDO 1,2-ETHANEDIOL × 1 CYN CYANIDE ION × 1 DMS DIMETHYL SULFOXIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions：pH 6；CRYSTALLISATION CONDITIONS: 22 % PEG 3000, 0.1 M KBR, 0.1 M CITRATE PH 3.6 CRYSTALS WERE SOAKED IN 50 MM KCN, 200 MM CYCLOPENTANEDIONE, 10 % DMSO, 22 % PEG3000, 0.1 M SODIUM CITRATE PH 6 FOR 10 MIN AT ROOM TMEPERATURE	Resolution 1.70 Å R-free 0.204

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 2CIY	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1CPO CHLOROPEROXIDASE Deposited 1996-02-10	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain A 22–319（298 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 MAN alpha-D-mannopyranose × 9 XYS alpha-D-xylopyranose × 1 MN MANGANESE (II) ION × 1 HEM PROTOPORPHYRIN IX CONTAINING FE × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.90 Å R-free 0.224
2CIV Chloroperoxidase bromide complex Deposited 2006-03-26	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain A 21–319（299 aa） Fragment：RESIDUES 21-319	Non-standard monomer：Yes (specific site not provided by mmCIF)	MN MANGANESE (II) ION × 1 HEM PROTOPORPHYRIN IX CONTAINING FE × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 MAN alpha-D-mannopyranose × 10 BR BROMIDE ION × 5	X-RAY DIFFRACTION X-ray crystallization conditions pH 3.6；22 % PEG3000, 0.1 M KBR, 0.1 M CITRATE PH 3.6	Resolution 1.80 Å R-free 0.184
2CIW Chloroperoxidase iodide complex Deposited 2006-03-26	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain A 21–319（299 aa） Fragment：RESIDUES 21-319	Non-standard monomer：Yes (specific site not provided by mmCIF)	MN MANGANESE (II) ION × 1 HEM PROTOPORPHYRIN IX CONTAINING FE × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 MAN alpha-D-mannopyranose × 11 IOD IODIDE ION × 7	X-RAY DIFFRACTION X-ray crystallization conditions pH 3.6；20 % PEG 3350, 50 MM NAI, 0.1 M SODIUM CITRATE PH 3.6	Resolution 1.15 Å R-free 0.171
2CIX chloroperoxidase complexed with cyclopentanedione Deposited 2006-03-26	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain A 21–319（299 aa） Fragment：RESIDUES 21-319	Non-standard monomer：Yes (specific site not provided by mmCIF)	MN MANGANESE (II) ION × 1 HEM PROTOPORPHYRIN IX CONTAINING FE × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 MAN alpha-D-mannopyranose × 10 EDO 1,2-ETHANEDIOL × 1 CEJ CYCLOPENTANE-1,3-DIONE × 1 BR BROMIDE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions pH 3.6；ML: 22 % PEG3000, 0.1 M KBR, 0.1 M CITRATE PH 3.6 CRYSTALS WERE SOAKED IN ML SUPPLEMENTED WITH 200 MM CYCLOPENTANEDIONE, 10 % DMSO	Resolution 1.80 Å R-free 0.217
2CIZ chloroperoxidase complexed with acetate Deposited 2006-03-26	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain A 21–319（299 aa） Fragment：RESIDUES 21-319	Non-standard monomer：Yes (specific site not provided by mmCIF)	MN MANGANESE (II) ION × 1 HEM PROTOPORPHYRIN IX CONTAINING FE × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 MAN alpha-D-mannopyranose × 9 EDO 1,2-ETHANEDIOL × 2 ACT ACETATE ION × 2 BR BROMIDE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions pH 3.6；CRYSTALS WERE SOAKED IN 300 MM ACETIC ACID, 50 MM KBR, 22 % PEG3000, 0.1 M CITRATE PH 3.6 FOR 10 MIN AT ROOM TEMPERATURE	Resolution 1.30 Å R-free 0.170
2CJ0 chloroperoxidase complexed with nitrate Deposited 2006-03-26	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain A 21–319（299 aa） Fragment：RESIDUES 21-319	Non-standard monomer：Yes (specific site not provided by mmCIF)	MN MANGANESE (II) ION × 1 HEM PROTOPORPHYRIN IX CONTAINING FE × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 MAN alpha-D-mannopyranose × 12 EDO 1,2-ETHANEDIOL × 3 NO3 NITRATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions 50 MM MG(NO3)2, 20 % PEG 3000, 0.1 M SODIUM CITRATE PH3.6	Resolution 1.75 Å R-free 0.207
2CJ1 chloroperoxidase complexed with formate (ethylene glycol cryoprotectant) Deposited 2006-03-26	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain A 21–319（299 aa） Fragment：RESIDUES 21-319	Non-standard monomer：Yes (specific site not provided by mmCIF)	MN MANGANESE (II) ION × 1 HEM PROTOPORPHYRIN IX CONTAINING FE × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 MAN alpha-D-mannopyranose × 12 EDO 1,2-ETHANEDIOL × 3 FMT FORMIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 3.6；100 MM SODIUM FORMATE, 24 % PEG 3000, 0.1 M CITRATE PH 3.6 CRYOPROTECTANT CONTAINED 15 % ETHYLENE GLYCOL	Resolution 1.70 Å R-free 0.229
2CJ2 chloroperoxidase complexed with formate (sugar cryoprotectant) Deposited 2006-03-26	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain A 21–319（299 aa） Fragment：RESIDUES 21-319	Non-standard monomer：Yes (specific site not provided by mmCIF)	MN MANGANESE (II) ION × 1 HEM PROTOPORPHYRIN IX CONTAINING FE × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 MAN alpha-D-mannopyranose × 10 FMT FORMIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 3.6；100 MM SODIUM FORMATE, 24 % PEG 3000, 0.1 M SODIUM CITRATE PH 3.6 CRYOPROTECTANT: ML SUPPLEMENTED WITH 10 % XYLITOL, 10 % SUCROSE	Resolution 1.60 Å R-free 0.204
2CPO CHLOROPEROXIDASE Deposited 1996-02-10	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain A 22–319（298 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 MAN alpha-D-mannopyranose × 8 MN MANGANESE (II) ION × 1 HEM PROTOPORPHYRIN IX CONTAINING FE × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.10 Å R-free 0.228
2J18 Chloroperoxidase mixture of ferric and ferrous states (low dose data set) Deposited 2006-08-09	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain A 22–319（298 aa） Fragment：RESIDUES 22-319	Non-standard monomer：Yes (specific site not provided by mmCIF)	MN MANGANESE (II) ION × 1 HEM PROTOPORPHYRIN IX CONTAINING FE × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 MAN alpha-D-mannopyranose × 9 BR BROMIDE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions pH 3.4；50MM KBR, 20% PEG3000, 0.1 M SODIUM CITRATE PH3.4, pH 3.40	Resolution 1.75 Å R-free 0.206
2J19 Ferrous Chloroperoxidase (high dose data set) Deposited 2006-08-09	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain A 22–319（298 aa） Fragment：RESIDUES 22-319	Non-standard monomer：Yes (specific site not provided by mmCIF)	MN MANGANESE (II) ION × 1 HEM PROTOPORPHYRIN IX CONTAINING FE × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 MAN alpha-D-mannopyranose × 9 BR BROMIDE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions pH 3.4；50MM KBR, 20% PEG3000, 0.1 SODIUM CITRATE PH 3.4	Resolution 1.75 Å R-free 0.204
2J5M Structure of Chloroperoxidase Compound 0 Deposited 2006-09-18	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain A 21–319（299 aa） Fragment：RESIDUES 21-319	Non-standard monomer：Yes (specific site not provided by mmCIF)	MN MANGANESE (II) ION × 1 HEM PROTOPORPHYRIN IX CONTAINING FE × 1 PEO HYDROGEN PEROXIDE × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 MAN alpha-D-mannopyranose × 10 EDO 1,2-ETHANEDIOL × 1 ACT ACETATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6；22 % PEG3000, 0.1 M KBR, 0.1 M NA CITRATE PH 3.6	Resolution 1.75 Å R-free 0.210
7RST The Crystal Structure of Recombinant Chloroperoxidase Expressed in Aspergillus niger Deposited 2021-08-11	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain A 21–319（299 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	MN MANGANESE (II) ION × 1 HEM PROTOPORPHYRIN IX CONTAINING FE × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 MAN alpha-D-mannopyranose × 12 IOD IODIDE ION × 10	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293.15 K；0.2M NaI, 20% polyethyleneglycol (PEG) 3350	Resolution 1.69 Å R-free 0.210

13 other PDB entries and 13 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	PRXC_CALFU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–299； UniProt 21–319

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	2ciy
Deposition date deposition_date	2006-03-26
Structure title title	Chloroperoxidase complexed with cyanide and DMSO
Keywords keywords	OXIDOREDUCTASE, HEME, IRON, CHLORIDE, MANGANESE, PEROXIDASE, PYRROLIDONE CARBOXYLIC ACID, GLYCOPROTEIN, METAL-BINDING; 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	19.78 Å
Radius of gyration Rg (electron density) rg_electron	18.58 Å
Forward intensity I(0) i0	24237100.00
Molecular weight molecular_weight	36840.0 kDa
Excluded volume excluded_volume	45500 Å³
Envelope volume envelope_volume	50641 Å³
Hydration-shell volume shell_volume	21941 Å³
Envelope diameter envelope_diameter	64.6 Å
Shell Rg shell_rg	25.75 Å
Envelope Rg envelope_rg	18.99 Å
Shape Rg shape_rg	18.54 Å
Total Rg total_rg	19.58 Å
Total atoms total_atoms	2585
Residues n_residues	298
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	60.6 Å
Rg (real space) rg_real	19.61 Å
Rg uncertainty (real space) rg_real_error	0.16 Å
I(0) (real space) i0_real	2.4240e+07
I(0) uncertainty (real space) i0_real_error	2.6260e+05
Rg (reciprocal space) rg_reciprocal	19.64 Å
I(0) (reciprocal space) i0_reciprocal	24240000.0000
Solution quality estimate total_estimate	0.6709
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	25.6 Å
Skewness Skewness skewness	0.103
Kurtosis Kurtosis kurtosis	-0.456
Angular range angular_range	— – 0.4000 Å⁻¹
Current regularization parameter α current_alpha	0.0011
Highest regularization parameter α highest_alpha	6282000.0000
Real-space data points n_real_points	72
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.911; Stabil: 1.000; Sysdev: 0.000; Positv: 1.000; Valcen: 0.987; Smooth: 0.999

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (12)

Entity 1 Entity 1 polymer

Description description	CHLOROPEROXIDASE
Molecular weight formula_weight	32746.9 kDa
EC 编号 ec_number	1.11.1.10
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	3030

QEPGSGIGYPYDNNTLPYVAPGPTDSRAPCPALNALANHGYIPHDGRAISRETLQNAFLNHMGIANSVIELALTNAFVVCEYVTGSDCGDSLVNLTLLAEPHAFEHDHSFSRKDYKQGVANSNDFIDNRNFDAETFQTSLDVVAGKTHFDYADMNEIRLQRESLSNELDFPGWFTESKPIQNVESGFIFALVSDFNLPDNDENPLVRIDWWKYWFTNESFPYHLGWHPPSPAREIEFVTSASSAVLAASVTSTPSSLPSGAIGPGAEAVPLSFASTMTPFLLATNAPYYAQDPTLGPND

Entity 2 Entity 2 branched

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	424.4 kDa
Source method src_method	man
Copy count entity_count	2

Entity 3 Entity 3 branched

Description description	alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose
Molecular weight formula_weight	342.3 kDa
Source method src_method	man
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	MANGANESE (II) ION
Molecular weight formula_weight	54.9 kDa
Source method src_method	syn
Copy count entity_count	1

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	1

Entity 6 Entity 6 non-polymer

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	221.2 kDa
Source method src_method	man
Copy count entity_count	1

Entity 7 Entity 7 non-polymer

Description description	alpha-D-mannopyranose
Molecular weight formula_weight	180.2 kDa
Source method src_method	man
Copy count entity_count	11

Entity 8 Entity 8 non-polymer

Description description	BROMIDE ION
Molecular weight formula_weight	79.9 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 9 Entity 9 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 10 Entity 10 non-polymer

Description description	CYANIDE ION
Molecular weight formula_weight	26.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 11 Entity 11 non-polymer

Description description	DIMETHYL SULFOXIDE
Molecular weight formula_weight	78.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 12 Entity 12 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	398

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7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d2ciya1
Class class	a — All alpha proteins
Fold Fold fold	a.39 — EF Hand-like
Superfamily Superfamily superfamily	a.39.3 — Cloroperoxidase
Family Family family	a.39.3.1 — Cloroperoxidase

Domain ID domain_id	d2ciya2
Class class	a — All alpha proteins
Fold Fold fold	a.39 — EF Hand-like
Superfamily Superfamily superfamily	a.39.3 — Cloroperoxidase
Family Family family	a.39.3.1 — Cloroperoxidase

CATH v4.4 (1 domains)

Domain ID domain_id	2ciyA00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	489 — Chloroperoxidase
Homologous superfamily homologous superfamily	10 — Chloroperoxidase-like

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8. Citations (1)

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Unit-cell length a length_a	58.210 Å
Unit-cell length b length_b	151.030 Å
Unit-cell length c length_c	101.110 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	C 2 2 21
Space-group number int_tables_number	20
Crystal system crystal_system	—

Resolution resolution	1.700 Å
Low-resolution limit resolution_low	19.840 Å
R factor r_factor	0.1800
R_work r_work	0.1790
R_free r_free	0.2040

fit	/app/data/saxs_computation/ci/2ciy/2ciy.fit
pddf	/app/data/pr_computation/ci/2ciy/2ciy.pr.out
profile	/app/data/saxs_computation/ci/2ciy/2ciy.dat