SAXSdb — 3qfs

▼

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

NADPH--cytochrome P450 reductase

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 241–677	Fragment：FAD/NADPH domain (UNP residues 241-677)	FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 NAP NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.8；292 K；100 mM magnesium chloride, 15% PEG5000 MME, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 292K	Resolution 1.40 Å R-free 0.231

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 3QFS	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1B1C CRYSTAL STRUCTURE OF THE FMN-BINDING DOMAIN OF HUMAN CYTOCHROME P450 REDUCTASE AT 1.93A RESOLUTION Deposited 1998-11-19	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 61–241（181 aa） Fragment：FMN-BINDING DOMAIN	Not recorded	CA CALCIUM ION × 1 FMN FLAVIN MONONUCLEOTIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；18-20% (W/V) PEG400, 100 MM HEPES (PH6.8-7.2), 200 MM CACL2 4 DEGREES C, pH 7.0	Resolution 1.93 Å R-free 0.243
3FJO Structure of chimeric YH CPR Deposited 2008-12-15	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 232–677（446 aa） Fragment：yeast FMN domain, UNP residues 44-211, human FAD domain CPR, UNP residues 232-677	Not recorded	FMN FLAVIN MONONUCLEOTIDE × 1 FAD FLAVIN-ADENINE DINUCLEOTIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；298 K；PEGII from Nextal condition G11, pH8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.50 Å R-free 0.290
3QE2 Crystal Structure of Human NADPH-Cytochrome P450 Reductase Deposited 2011-01-19	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 64–677（614 aa） Fragment：UNP residues 64-677	Not recorded	FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 FMN FLAVIN MONONUCLEOTIDE × 1 NAP NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 1 CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；292 K；100 mM MES, 50 mM calcium acetate, 0.5 M sodium chloride, 14% PEG4000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 292KK	Resolution 1.75 Å R-free 0.239
3QE2 Crystal Structure of Human NADPH-Cytochrome P450 Reductase Deposited 2011-01-19	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 64–677（614 aa） Fragment：UNP residues 64-677	Not recorded	FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 FMN FLAVIN MONONUCLEOTIDE × 1 NAP NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；292 K；100 mM MES, 50 mM calcium acetate, 0.5 M sodium chloride, 14% PEG4000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 292KK	Resolution 1.75 Å R-free 0.239
3QFC Crystal Structure of Human NADPH-Cytochrome P450 (V492E mutant) Deposited 2011-01-21	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 64–677（614 aa） Fragment：UNP residues 64-677	Mutation：V489E	FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 FMN FLAVIN MONONUCLEOTIDE × 1 NAP NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 1 CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；292 K；100 mM MES, 50 mM calcium acetate, 0.5 M sodium chloride, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 292KK	Resolution 1.80 Å R-free 0.265
3QFC Crystal Structure of Human NADPH-Cytochrome P450 (V492E mutant) Deposited 2011-01-21	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 64–677（614 aa） Fragment：UNP residues 64-677	Mutation：V489E	FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 FMN FLAVIN MONONUCLEOTIDE × 1 NAP NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；292 K；100 mM MES, 50 mM calcium acetate, 0.5 M sodium chloride, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 292KK	Resolution 1.80 Å R-free 0.265
3QFR Crystal Structure of Human NADPH-Cytochrome P450 Reductase (R457H Mutant) Deposited 2011-01-22	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 64–677（614 aa） Fragment：UNP residues 64-677	Mutation：R454H	FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 FMN FLAVIN MONONUCLEOTIDE × 1 NAP NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 1 CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；292 K；100 mM MES, 50 mM calcium acetate, 0.1 M sodium chloride, 14% PEG4000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K	Resolution 2.40 Å R-free 0.285
3QFR Crystal Structure of Human NADPH-Cytochrome P450 Reductase (R457H Mutant) Deposited 2011-01-22	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 64–677（614 aa） Fragment：UNP residues 64-677	Mutation：R454H	FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 FMN FLAVIN MONONUCLEOTIDE × 1 NAP NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；292 K；100 mM MES, 50 mM calcium acetate, 0.1 M sodium chloride, 14% PEG4000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K	Resolution 2.40 Å R-free 0.285
3QFT Crystal Structure of NADPH-Cytochrome P450 Reductase (FAD/NADPH domain and R457H Mutant) Deposited 2011-01-22	Different mutation/modification Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 241–677（437 aa） Fragment：FAD/NADPH domain (UNP residues 241-677)	Mutation：R454H	FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 NAP NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.8；292 K；100 mM magnesium chloride, 15% PEG5000 MME, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 292K	Resolution 1.40 Å R-free 0.227
5EMN Crystal Structure of Human NADPH-Cytochrome P450 Reductase(A287P mutant) Deposited 2015-11-06	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 64–677（614 aa） Fragment：UNP residues 57-677	Mutation：P228L, A287P, A503V	FMN FLAVIN MONONUCLEOTIDE × 1 FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 NAP NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；292 K；100mM MES,pH6.5,50mM CaAc2,0.1M NaCl, 14% PEG4K	Resolution 2.20 Å R-free 0.277
5EMN Crystal Structure of Human NADPH-Cytochrome P450 Reductase(A287P mutant) Deposited 2015-11-06	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 64–677（614 aa） Fragment：UNP residues 57-677	Mutation：P228L, A287P, A503V	FMN FLAVIN MONONUCLEOTIDE × 1 FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 NAP NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；292 K；100mM MES,pH6.5,50mM CaAc2,0.1M NaCl, 14% PEG4K	Resolution 2.20 Å R-free 0.277
5FA6 wild type human CYPOR Deposited 2015-12-11	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 64–677（614 aa） Fragment：UNP residues 64-677	Not recorded	FMN FLAVIN MONONUCLEOTIDE × 1 FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 NAP NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；292 K；MES buffer, PEG 4K, CaAc2 and NaCl	Resolution 2.30 Å R-free 0.280
5FA6 wild type human CYPOR Deposited 2015-12-11	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 64–677（614 aa） Fragment：UNP residues 64-677	Not recorded	FMN FLAVIN MONONUCLEOTIDE × 1 FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 NAP NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；292 K；MES buffer, PEG 4K, CaAc2 and NaCl	Resolution 2.30 Å R-free 0.280

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

View Construct and Data Evidence

UniProt name	NCPR_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 22–458； UniProt 241–677

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	3qfs
Deposition date deposition_date	2011-01-22
Structure title title	Crystal Structure of NADPH-Cytochrome P450 Reductase (FAD/NADPH domain)
Keywords keywords	NADPH-Cytochrome P450 Reductase, flavoprotein, FAD, NADPH, OXIDOREDUCTASE; OXIDOREDUCTASE
Experimental Method method	X-RAY DIFFRACTION

▼

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

Radius of gyration Rg (Guinier) rg_guinier	25.78 Å
Radius of gyration Rg (electron density) rg_electron	24.98 Å
Forward intensity I(0) i0	45115200.00
Molecular weight molecular_weight	50636.0 kDa
Excluded volume excluded_volume	62844 Å³
Envelope volume envelope_volume	77314 Å³
Hydration-shell volume shell_volume	26067 Å³
Envelope diameter envelope_diameter	84.8 Å
Shell Rg shell_rg	31.90 Å
Envelope Rg envelope_rg	25.02 Å
Shape Rg shape_rg	24.98 Å
Total Rg total_rg	25.76 Å
Total atoms total_atoms	3560
Residues n_residues	435
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

▼

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

Maximum dimension Dmax dmax	81.9 Å
Rg (real space) rg_real	25.77 Å
Rg uncertainty (real space) rg_real_error	0.55 Å
I(0) (real space) i0_real	4.5120e+07
I(0) uncertainty (real space) i0_real_error	6.7400e+05
Rg (reciprocal space) rg_reciprocal	25.78 Å
I(0) (reciprocal space) i0_reciprocal	45120000.0000
Solution quality estimate total_estimate	0.9050
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	27.8 Å
Skewness Skewness skewness	0.302
Kurtosis Kurtosis kurtosis	-0.516
Angular range angular_range	— – 0.3100 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	6816000.0000
Real-space data points n_real_points	63
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.929; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.994; Smooth: 0.978

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	NADPH--cytochrome P450 reductase
Molecular weight formula_weight	52003.1 kDa
EC 编号 ec_number	1.6.2.4
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	3984

MGSSHHHHHHSSGLVPRGSHMSIRQYELVVHTDIDAAKVYMGEMGRLKSYENQKPPFDAKNPFLAAVTTNRKLNQGTERHLMHLELDISDSKIRYESGDHVAVYPANDSALVNQLGKILGADLDVVMSLNNLDEESNKKHPFPCPTSYRTALTYYLDITNPPRTNVLYELAQYASEPSEQELLRKMASSSGEGKELYLSWVVEARRHILAILQDCPSLRPPIDHLCELLPRLQARYYSIASSSKVHPNSVHICAVVVEYETKAGRINKGVATNWLRAKEPVGENGGRALVPMFVRKSQFRLPFKATTPVIMVGPGTGVAPFIGFIQERAWLRQQGKEVGETLLYYGCRRSDEDYLYREELAQFHRDGALTQLNVAFSREQSHKVYVQHLLKQDREHLWKLIEGGAHIYVCGDARNMARDVQNTFYDIVAELGAMEHAQAVDYIKKLMTKGRYSLDVWS

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	FLAVIN-ADENINE DINUCLEOTIDE
Molecular weight formula_weight	785.5 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
Molecular weight formula_weight	743.4 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	424

▼

7. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d3qfsa1
Class class	b — All beta proteins
Fold Fold fold	b.43 — Reductase/isomerase/elongation factor common domain
Superfamily Superfamily superfamily	b.43.4 — Riboflavin synthase domain-like
Family Family family	b.43.4.1 — NADPH-cytochrome p450 reductase FAD-binding domain-like

Domain ID domain_id	d3qfsa2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.25 — Ferredoxin reductase-like, C-terminal NADP-linked domain
Superfamily Superfamily superfamily	c.25.1 — Ferredoxin reductase-like, C-terminal NADP-linked domain
Family Family family	c.25.1.0 — automated matches

CATH v4.4 (3 domains)

Domain ID domain_id	3qfsA01
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	30 — Elongation Factor Tu (Ef-tu); domain 3
Homologous superfamily homologous superfamily	10 — Translation factors

Domain ID domain_id	3qfsA02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	990 — NADPH-cytochrome p450 Reductase; Chain A, domain 3
Homologous superfamily homologous superfamily	10 — NADPH-cytochrome p450 Reductase; Chain A, domain 3

Domain ID domain_id	3qfsA03
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	80 — Nucleotide-binding domain of ferredoxin-NADP reductase (FNR) module

▶

8. Citations (1)

▶

Unit-cell length a length_a	54.640 Å
Unit-cell length b length_b	58.540 Å
Unit-cell length c length_c	130.280 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	1.400 Å
Low-resolution limit resolution_low	19.710 Å
R factor r_factor	0.2110
R_work r_work	0.2110
R_free r_free	0.2310

fit	/app/data/saxs_computation/qf/3qfs/3qfs.fit
pddf	/app/data/pr_computation/qf/3qfs/3qfs.pr.out
profile	/app/data/saxs_computation/qf/3qfs/3qfs.dat

Crystal Structure of NADPH-Cytochrome P450 Reductase (FAD/NADPH domain)

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

NADPH--cytochrome P450 reductase

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