3qfc

Crystal Structure of Human NADPH-Cytochrome P450 (V492E mutant)

Method: X-RAY DIFFRACTION Dmax: 118.4 Å Quality: EXCELLENT

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

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.

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 3qfc

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 3qfc
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2. Structure Basics 2. Structure Basics

Entry ID entry_id3qfc
Deposition date deposition_date2011-01-21
Structure title titleCrystal Structure of Human NADPH-Cytochrome P450 (V492E mutant)
Keywords keywordshuman CYPOR, cytochrome P450 reductase, flavoprotein, FAD, FMN, NADPH, OXIDOREDUCTASE; OXIDOREDUCTASE
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier37.04
Radius of gyration Rg (electron density) rg_electron36.59
Forward intensity I(0) i0313919000.00
Molecular weight molecular_weight140060.0 kDa
Excluded volume excluded_volume173520 ų
Envelope volume envelope_volume224140 ų
Hydration-shell volume shell_volume50647 ų
Envelope diameter envelope_diameter120.7
Shell Rg shell_rg43.31
Envelope Rg envelope_rg35.95
Shape Rg shape_rg36.60
Total Rg total_rg36.99
Total atoms total_atoms9853
Residues n_residues1202
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 −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

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

Maximum dimension Dmax dmax118.4
Rg (real space) rg_real36.96
Rg uncertainty (real space) rg_real_error0.70
I(0) (real space) i0_real3.1390e+08
I(0) uncertainty (real space) i0_real_error5.2450e+06
Rg (reciprocal space) rg_reciprocal37.01
I(0) (reciprocal space) i0_reciprocal313900000.0000
Solution quality estimate total_estimate0.9051
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary41.3
Skewness Skewness skewness0.215
Kurtosis Kurtosis kurtosis-0.646
Angular range angular_range— – 0.2150 −1
Current regularization parameter α current_alpha0.0001
Highest regularization parameter α highest_alpha94670000.0000
Real-space data points n_real_points44
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.940; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.990; Smooth: 0.951

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (6)

7. Fold Classification (SCOP + CATH) 14 domains

SCOP 2.08 (6 domains)

Domain ID domain_idd3qfca1
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_idd3qfca2
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_idd3qfca3
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_idd3qfcb1
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_idd3qfcb2
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_idd3qfcb3
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_id3qfcA01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily360 — Flavodoxin domain
Domain ID domain_id3qfcA02
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_id3qfcA03
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_id3qfcA04
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_id3qfcB01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily360 — Flavodoxin domain
Domain ID domain_id3qfcB02
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_id3qfcB03
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_id3qfcB04
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

8. Citations (1)

9. Files and Curves (10)