SAXSdb — 6bpv

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

Cysteine dioxygenase type 1

Homo sapiens

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 2–200	Non-standard monomer：Yes (specific site not provided by mmCIF)	FE2 FE (II) ION × 1 CYS CYSTEINE × 1 SO4 SULFATE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.5；295 K；0.1 M MES, 2 M ammonium sulfate, 2% PEG400	Resolution 1.95 Å R-free 0.179

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 6BPV	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2IC1 Crystal Structure of Human Cysteine Dioxygenase in Complex with Substrate Cysteine Deposited 2006-09-12	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 1–200（200 aa）	Not recorded	FE2 FE (II) ION × 1 CYS CYSTEINE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；289 K；0.1 M Sodium cacodylate, 0.2 M Magnesium chloride, 17.6% PEG 8000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K	Resolution 2.70 Å R-free 0.215
6BGF Crystal structure of cysteine-bound ferrous form of the crosslinked human cysteine dioxygenase Deposited 2017-10-28	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 2–200（199 aa）	Not recorded	CYS CYSTEINE × 1 FE2 FE (II) ION × 1 SO4 SULFATE ION × 3 GOL GLYCEROL × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；295 K；0.1 M MES, 2 M ammonium sulfate, 2% PEG400	Resolution 2.25 Å R-free 0.219
6BGM Crystal structure of ferrous form of the crosslinked human cysteine dioxygenase Deposited 2017-10-28	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 2–200（199 aa）	Not recorded	FE2 FE (II) ION × 1 SO4 SULFATE ION × 3 GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；295 K；0.1 M MES, 2 M ammonium sulfate, 2% PEG400	Resolution 2.21 Å R-free 0.216
6BPR Crystal structure of cysteine, nitric oxide-bound ferrous form of the uncrosslinked F2-Tyr157 human cysteine dioxygenase Deposited 2017-11-26	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2–200（199 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	FE FE (III) ION × 1 CYS CYSTEINE × 1 NO NITRIC OXIDE × 1 SO4 SULFATE ION × 3 GOL GLYCEROL × 7	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；295 K；0.1 M MES, 2 M ammonium sulfate, 2% PEG400	Resolution 1.96 Å R-free 0.188
6BPS Crystal structure of cysteine-bound ferrous form of the uncrosslinked F2-Tyr157 human cysteine dioxygenase Deposited 2017-11-26	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2–200（199 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	FE2 FE (II) ION × 1 CYS CYSTEINE × 1 SO4 SULFATE ION × 3 GOL GLYCEROL × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；295 K；0.1 M MES, 2 M ammonium sulfate, 2% PEG400	Resolution 2.10 Å R-free 0.203
6BPT Crystal structure of ferrous form of the uncrosslinked F2-Tyr157 human cysteine dioxygenase Deposited 2017-11-26	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2–200（199 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	FE2 FE (II) ION × 1 SO4 SULFATE ION × 4 GOL GLYCEROL × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；295 K；0.1 M MES, 2 M ammonium sulfate, 2% PEG400	Resolution 2.40 Å R-free 0.202
6BPU Crystal structure of ferrous form of the F2-Tyr157 human cysteine dioxygenase with both uncrosslinked and crosslinked cofactor Deposited 2017-11-26	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2–200（199 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	FE2 FE (II) ION × 1 SO4 SULFATE ION × 3 GOL GLYCEROL × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；295 K；0.1 M MES, 2 M ammonium sulfate, 2% PEG400	Resolution 1.80 Å R-free 0.189
6BPW Crystal structure of ferrous form of the Cl2-Tyr157 human cysteine dioxygenase with both uncrosslinked and crosslinked cofactor Deposited 2017-11-26	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2–200（199 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	FE2 FE (II) ION × 1 GOL GLYCEROL × 6 SO4 SULFATE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；295 K；0.1 M MES, 2 M ammonium sulfate, 2% PEG400	Resolution 2.43 Å R-free 0.206
6BPX Crystal structure of cysteine-bound ferrous form of the matured Cl2-Tyr157 human cysteine dioxygenase Deposited 2017-11-26	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2–200（199 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	FE2 FE (II) ION × 1 CYS CYSTEINE × 1 SO4 SULFATE ION × 3 GOL GLYCEROL × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；295 K；0.1 M MES, 2 M ammonium sulfate, 2% PEG400	Resolution 2.15 Å R-free 0.212
6CDH Crystal structure of ferrous form of the Cl-Tyr157 human cysteine dioxygenase with both uncrosslinked and crosslinked cofactor Deposited 2018-02-08	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2–200（199 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	FE2 FE (II) ION × 1 SO4 SULFATE ION × 3 GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；295 K；0.1 M MES, 2 M ammonium sulfate, 2% PEG400	Resolution 1.82 Å R-free 0.182
6CDN Crystal structure of cysteine-bound ferrous form of the crosslinked Cl-Tyr157 human cysteine dioxygenase Deposited 2018-02-08	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2–200（199 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	CYS CYSTEINE × 1 FE2 FE (II) ION × 1 SO4 SULFATE ION × 3 GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；295 K；0.1 M MES, 2 M ammonium sulfate, 2% PEG400	Resolution 2.06 Å R-free 0.193
6E87 Crystal structure of ferrous form of the crosslinked human cysteine dioxygenase in the anaerobic condition Deposited 2018-07-27	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 2–200（199 aa）	Not recorded	FE2 FE (II) ION × 1 SO4 SULFATE ION × 3 GOL GLYCEROL × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；295 K；0.1 M MES, 2 M ammonium sulfate, 2% PEG400	Resolution 1.95 Å R-free 0.197
6N42 Crystal structure of cysteine-bound ferrous form of the crosslinked human cysteine dioxygenase in the anaerobic condition Deposited 2018-11-16	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 2–200（199 aa）	Not recorded	FE2 FE (II) ION × 1 CYS CYSTEINE × 1 GOL GLYCEROL × 5 SO4 SULFATE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；295 K；0.1 M MES, 2 M ammonium sulfate, 2% PEG400	Resolution 2.20 Å R-free 0.210
6N43 Crystal structure of cysteine, nitric oxide-bound ferrous form of the crosslinked human cysteine dioxygenase in the anaerobic condition Deposited 2018-11-16	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 2–200（199 aa）	Not recorded	CYS CYSTEINE × 1 FE FE (III) ION × 1 NO NITRIC OXIDE × 1 SO4 SULFATE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；295 K；0.1 M MES, 2 M ammonium sulfate, 2% PEG400	Resolution 2.29 Å R-free 0.213
8VL9 Crystal structure of EloBC-VHL-CDO1 complex bound to compound 8 molecular glue Deposited 2024-01-11	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain D 1–200（200 aa）	Not recorded	A1ACI N-acetyl-3-methyl-L-valyl-(4R)-4-hydroxy-N-{[(4P)-4-(1H-pyrazol-3-yl)naphthalen-1-yl]methyl}-L-prolinamide × 1 CIT CITRIC ACID × 1 FE2 FE (II) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；294 K；0.2M SODIUM CITRATE, 0.1M BIS-TRIS-PROPANE PH 6.5, 20% PEG3350	Resolution 2.50 Å R-free 0.216
8VLB Crystal structure of EloBC-VHL-CDO1 complex bound to compound 4 molecular glue Deposited 2024-01-11	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain D 1–200（200 aa）	Not recorded	3JF N-acetyl-3-methyl-L-valyl-(4R)-4-hydroxy-N-[4-(4-methyl-1,3-thiazol-5-yl)benzyl]-L-prolinamide × 1 CIT CITRIC ACID × 1 FE2 FE (II) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；294 K；0.2M SODIUM CITRATE, 0.1M BIS-TRIS-PROPANE PH 6.5, 20% PEG3350	Resolution 2.90 Å R-free 0.258
9T7V Structure of LRRC58-EloB/C-CDO1 in complex with NEDD8-CUL5-RBX2-ARIH2-Ub Deposited 2025-11-12	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric	Chain A 1–200（200 aa）	Mutation：K8C, C76A, C93S, C130A, C164S	FE FE (III) ION × 1 SY8 5-azanylpentan-2-one × 1 ZN ZINC ION × 8	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.95 Å

17 other PDB entries and 17 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	CDO1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–200； UniProt 2–200

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	6bpv
Deposition date deposition_date	2017-11-26
Structure title title	Crystal structure of cysteine-bound ferrous form of the matured F2-Tyr157 human cysteine dioxygenase
Keywords keywords	Cysteine, Cys-Tyr cofactor, iron, unnatural amino acid, OXIDOREDUCTASE; 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	17.45 Å
Radius of gyration Rg (electron density) rg_electron	16.35 Å
Forward intensity I(0) i0	9754370.00
Molecular weight molecular_weight	21861.0 kDa
Excluded volume excluded_volume	26817 Å³
Envelope volume envelope_volume	31105 Å³
Hydration-shell volume shell_volume	15976 Å³
Envelope diameter envelope_diameter	56.2 Å
Shell Rg shell_rg	22.43 Å
Envelope Rg envelope_rg	16.72 Å
Shape Rg shape_rg	16.35 Å
Total Rg total_rg	17.33 Å
Total atoms total_atoms	1529
Residues n_residues	186
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	55.5 Å
Rg (real space) rg_real	17.36 Å
Rg uncertainty (real space) rg_real_error	0.32 Å
I(0) (real space) i0_real	9.7540e+06
I(0) uncertainty (real space) i0_real_error	1.1530e+05
Rg (reciprocal space) rg_reciprocal	17.37 Å
I(0) (reciprocal space) i0_reciprocal	9754000.0000
Solution quality estimate total_estimate	0.8137
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	22.2 Å
Skewness Skewness skewness	0.216
Kurtosis Kurtosis kurtosis	-0.299
Angular range angular_range	— – 0.4550 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	2109000.0000
Real-space data points n_real_points	76
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.859; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.000

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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	Cysteine dioxygenase type 1
Molecular weight formula_weight	22981.7 kDa
EC 编号 ec_number	1.13.11.20
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	1770

SEQTEVLKPRTLADLIRILHQLFAGDEVNVEEVQAIMEAYESDPTEWAMYAKFDQYRYTRNLVDQGNGKFNLMILCWGEGHGSSIHDHTNSHCFLKMLQGNLKETLFAWPDKKSNEMVKKSERVLRENQCAYINDSVGLHRVENISHTEPAVSLHLXSPPFDTCHAFDQRTGHKNKVTMTFHSKFGIRTPNATSGSLENN

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	Human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	FE (II) ION
Molecular weight formula_weight	55.8 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	CYSTEINE
Molecular weight formula_weight	121.2 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	3

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	169

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d6bpva_
Class class	b — All beta proteins
Fold Fold fold	b.82 — Double-stranded beta-helix
Superfamily Superfamily superfamily	b.82.1 — RmlC-like cupins
Family Family family	b.82.1.19 — Cysteine dioxygenase type I

CATH v4.4 (1 domains)

Domain ID domain_id	6bpvA00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	10 — Jelly Rolls

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8. Citations (1)

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Unit-cell length a length_a	131.435 Å
Unit-cell length b length_b	131.435 Å
Unit-cell length c length_c	34.177 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	6

Space group space_group	P 65
Space-group number int_tables_number	170
Crystal system crystal_system	—

Resolution resolution	1.950 Å
Low-resolution limit resolution_low	31.570 Å
R factor r_factor	0.1619
R_work r_work	0.1604
R_free r_free	0.1792

fit	/app/data/saxs_computation/bp/6bpv/6bpv.fit
pddf	/app/data/pr_computation/bp/6bpv/6bpv.pr.out
profile	/app/data/saxs_computation/bp/6bpv/6bpv.dat

Crystal structure of cysteine-bound ferrous form of the matured F2-Tyr157 human cysteine dioxygenase

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

Cysteine dioxygenase type 1

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