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5emn

Crystal Structure of Human NADPH-Cytochrome P450 Reductase(A287P mutant)

Method: X-RAY DIFFRACTION Dmax: 119.3 Å Quality: EXCELLENT
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1. Protein Identity and Related Structures Protein Identity & Related Structures

NADPH--cytochrome P450 reductase

Homo sapiens

UniProt P16435

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 64–677 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
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain B； UniProt 64–677 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

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 5EMN 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 mutation/modification 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 mutation/modification 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 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
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 mutation/modification 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 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 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
3QFS Crystal Structure of NADPH-Cytochrome P450 Reductase (FAD/NADPH domain) 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 241–677（437 aa） Fragment：FAD/NADPH domain (UNP residues 241-677)
Not recorded 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
3QFT Crystal Structure of NADPH-Cytochrome P450 Reductase (FAD/NADPH domain and 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 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
5FA6 wild type human CYPOR Deposited 2015-12-11 Different construct Different mutation/modification 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 mutation/modification 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 12 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 5–618； UniProt 64–677 Author chain B； PDBConstruct 5–618； UniProt 64–677

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.

SAXS scattering curve SAXS Profile

SAXS profile for 5emn

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 5emn
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2. Structure Basics 2. Structure Basics

Entry ID entry_id5emn
Deposition date deposition_date2015-11-06
Structure title titleCrystal Structure of Human NADPH-Cytochrome P450 Reductase(A287P mutant)
Keywords keywordshuman CYPOR, ABS-like Phenotype, FLAVOPROTEIN, CYTOCHROME P450 REDUCTASE, OXIDOREDUCTASE; OXIDOREDUCTASE
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier37.21 Å
Radius of gyration Rg (electron density) rg_electron36.76 Å
Forward intensity I(0) i0312742000.00
Molecular weight molecular_weight139960.0 kDa
Excluded volume excluded_volume173480 ų
Envelope volume envelope_volume225920 ų
Hydration-shell volume shell_volume50755 ų
Envelope diameter envelope_diameter121.0 Å
Shell Rg shell_rg43.50 Å
Envelope Rg envelope_rg36.13 Å
Shape Rg shape_rg36.77 Å
Total Rg total_rg37.14 Å
Total atoms total_atoms9848
Residues n_residues1204
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax119.3 Å
Rg (real space) rg_real37.14 Å
Rg uncertainty (real space) rg_real_error0.78 Å
I(0) (real space) i0_real3.1270e+08
I(0) uncertainty (real space) i0_real_error5.2850e+06
Rg (reciprocal space) rg_reciprocal37.19 Å
I(0) (reciprocal space) i0_reciprocal312800000.0000
Solution quality estimate total_estimate0.9053
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary42.6 Å
Skewness Skewness skewness0.213
Kurtosis Kurtosis kurtosis-0.654
Angular range angular_range— – 0.2100 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha81180000.0000
Real-space data points n_real_points43
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.937; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.953
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

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7. Fold Classification (SCOP + CATH) 14 domains

SCOP 2.08 (6 domains)

Domain ID domain_idd5emna1
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.23 — Flavodoxin-like
Superfamily Superfamily superfamilyc.23.5 — Flavoproteins
Family Family familyc.23.5.0 — automated matches
Domain ID domain_idd5emna2
Class classb — All beta proteins
Fold Fold foldb.43 — Reductase/isomerase/elongation factor common domain
Superfamily Superfamily superfamilyb.43.4 — Riboflavin synthase domain-like
Family Family familyb.43.4.1 — NADPH-cytochrome p450 reductase FAD-binding domain-like
Domain ID domain_idd5emna3
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.25 — Ferredoxin reductase-like, C-terminal NADP-linked domain
Superfamily Superfamily superfamilyc.25.1 — Ferredoxin reductase-like, C-terminal NADP-linked domain
Family Family familyc.25.1.0 — automated matches
Domain ID domain_idd5emnb1
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.23 — Flavodoxin-like
Superfamily Superfamily superfamilyc.23.5 — Flavoproteins
Family Family familyc.23.5.0 — automated matches
Domain ID domain_idd5emnb2
Class classb — All beta proteins
Fold Fold foldb.43 — Reductase/isomerase/elongation factor common domain
Superfamily Superfamily superfamilyb.43.4 — Riboflavin synthase domain-like
Family Family familyb.43.4.1 — NADPH-cytochrome p450 reductase FAD-binding domain-like
Domain ID domain_idd5emnb3
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.25 — Ferredoxin reductase-like, C-terminal NADP-linked domain
Superfamily Superfamily superfamilyc.25.1 — Ferredoxin reductase-like, C-terminal NADP-linked domain
Family Family familyc.25.1.0 — automated matches

CATH v4.4 (8 domains)

Domain ID domain_id5emnA01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily360 — Flavodoxin domain
Domain ID domain_id5emnA02
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology30 — Elongation Factor Tu (Ef-tu); domain 3
Homologous superfamily homologous superfamily10 — Translation factors
Domain ID domain_id5emnA03
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology990 — NADPH-cytochrome p450 Reductase; Chain A, domain 3
Homologous superfamily homologous superfamily10 — NADPH-cytochrome p450 Reductase; Chain A, domain 3
Domain ID domain_id5emnA04
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily80 — Nucleotide-binding domain of ferredoxin-NADP reductase (FNR) module
Domain ID domain_id5emnB01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily360 — Flavodoxin domain
Domain ID domain_id5emnB02
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology30 — Elongation Factor Tu (Ef-tu); domain 3
Homologous superfamily homologous superfamily10 — Translation factors
Domain ID domain_id5emnB03
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology990 — NADPH-cytochrome p450 Reductase; Chain A, domain 3
Homologous superfamily homologous superfamily10 — NADPH-cytochrome p450 Reductase; Chain A, domain 3
Domain ID domain_id5emnB04
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily80 — Nucleotide-binding domain of ferredoxin-NADP reductase (FNR) module
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8. Citations (1)

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9. Files and Curves (10)