3ben

Structure of N-(12-imidazolyl-dodecanoyl)-L-leucine inhibitor bound to the heme domain of Cytochrome P450-BM3

Method: X-RAY DIFFRACTION Dmax: 101.5 Å Quality: GOOD

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

Cytochrome P450 102

Bacillus megaterium

UniProt P14779

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 1–470 Not recorded HEM PROTOPORPHYRIN IX CONTAINING FE × 1 LEH N-[12-(1H-imidazol-1-yl)dodecanoyl]-L-leucine × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 6;277 K;11% (w/v) PEG-3350, 200 mM magnesium chloride, 7.5% (v/v) glycerol, 100 mM MES, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K Resolution 1.65 Å R-free 0.191
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain B; UniProt 1–470 Not recorded HEM PROTOPORPHYRIN IX CONTAINING FE × 1 LEH N-[12-(1H-imidazol-1-yl)dodecanoyl]-L-leucine × 1 MG MAGNESIUM ION × 1 MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 6;277 K;11% (w/v) PEG-3350, 200 mM magnesium chloride, 7.5% (v/v) glycerol, 100 mM MES, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K Resolution 1.65 Å R-free 0.191

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.

168 other PDB entries and 310 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name CPXB_BACME
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–470; UniProt 1–470 Author chain B; PDBConstruct 1–470; UniProt 1–470

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 3ben

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id3ben
Deposition date deposition_date2007-11-19
Structure title titleStructure of N-(12-imidazolyl-dodecanoyl)-L-leucine inhibitor bound to the heme domain of Cytochrome P450-BM3
Keywords keywords;PROTEIN-SUBSTRATE COMPLEX, HEMEPROTEIN, Electron transport, FAD, Flavoprotein, FMN, Iron, Membrane, Metal-binding, Monooxygenase, Multifunctional enzyme, NADP, Oxidoreductase, Transport ;; OXIDOREDUCTASE
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier32.24
Radius of gyration Rg (electron density) rg_electron31.20
Forward intensity I(0) i0169972000.00
Molecular weight molecular_weight106240.0 kDa
Excluded volume excluded_volume133780 ų
Envelope volume envelope_volume163250 ų
Hydration-shell volume shell_volume42879 ų
Envelope diameter envelope_diameter109.6
Shell Rg shell_rg38.94
Envelope Rg envelope_rg31.18
Shape Rg shape_rg31.21
Total Rg total_rg31.81
Total atoms total_atoms7485
Residues n_residues911
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 dmax101.5
Rg (real space) rg_real32.19
Rg uncertainty (real space) rg_real_error0.59
I(0) (real space) i0_real1.7000e+08
I(0) uncertainty (real space) i0_real_error2.4770e+06
Rg (reciprocal space) rg_reciprocal32.21
I(0) (reciprocal space) i0_reciprocal170000000.0000
Solution quality estimate total_estimate0.8977
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary37.3
Skewness Skewness skewness0.301
Kurtosis Kurtosis kurtosis-0.443
Angular range angular_range— – 0.2450 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha41130000.0000
Real-space data points n_real_points50
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.926; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.889

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (6)

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd3bena_
Class classa — All alpha proteins
Fold Fold folda.104 — Cytochrome P450
Superfamily Superfamily superfamilya.104.1 — Cytochrome P450
Family Family familya.104.1.1 — Cytochrome P450
Domain ID domain_idd3benb_
Class classa — All alpha proteins
Fold Fold folda.104 — Cytochrome P450
Superfamily Superfamily superfamilya.104.1 — Cytochrome P450
Family Family familya.104.1.1 — Cytochrome P450

CATH v4.4 (2 domains)

Domain ID domain_id3benA00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology630 — Cytochrome p450
Homologous superfamily homologous superfamily10 — Cytochrome P450
Domain ID domain_id3benB00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology630 — Cytochrome p450
Homologous superfamily homologous superfamily10 — Cytochrome P450

8. Citations (4)

9. Files and Curves (10)