4k5k

Structure of bovine endothelial nitric oxide synthase heme domain in complex with ((2S, 3S)-1,3-bis((6-(2,5-dimethyl-1H-pyrrol-1-yl)-4-methylpyridin-2-yl)methoxy)-2-aminobutane

Method: X-RAY DIFFRACTION Dmax: 94.1 Å Quality: EXCELLENT

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

Nitric oxide synthase, endothelial

Bos taurus

UniProt P29473

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 homooligomer Homooligomer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain A; UniProt 40–482 Chain B; UniProt 40–482 Fragment:heme domain (UNP residues 40-482) Non-standard monomer:Yes (specific site not provided by mmCIF) HEM PROTOPORPHYRIN IX CONTAINING FE × 2 H4B 5,6,7,8-TETRAHYDROBIOPTERIN × 2 Q13 6,6'-{[(2S,3S)-2-aminobutane-1,3-diyl]bis(oxymethanediyl)}bis(4-methylpyridin-2-amine) × 2 ACT ACETATE ION × 4 GOL GLYCEROL × 2 ZN ZINC ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 6;277 K;18-22% PEG3350, 0.1 M cacodylate, 0.2 M magnesium acetate, 5 mM TCEP, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K Resolution 2.00 Å R-free 0.217

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.

125 other PDB entries and 125 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name NOS3_BOVIN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–443; UniProt 40–482 Author chain B; PDBConstruct 1–443; UniProt 40–482

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 4k5k

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 4k5k
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2. Structure Basics 2. Structure Basics

Entry ID entry_id4k5k
Deposition date deposition_date2013-04-14
Structure title titleStructure of bovine endothelial nitric oxide synthase heme domain in complex with ((2S, 3S)-1,3-bis((6-(2,5-dimethyl-1H-pyrrol-1-yl)-4-methylpyridin-2-yl)methoxy)-2-aminobutane
Keywords keywordsnitric oxide synthase, OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR complex; OXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier29.87
Radius of gyration Rg (electron density) rg_electron29.00
Forward intensity I(0) i0142585000.00
Molecular weight molecular_weight94353.0 kDa
Excluded volume excluded_volume117680 ų
Envelope volume envelope_volume141250 ų
Hydration-shell volume shell_volume40107 ų
Envelope diameter envelope_diameter93.5
Shell Rg shell_rg36.95
Envelope Rg envelope_rg29.11
Shape Rg shape_rg29.02
Total Rg total_rg29.64
Total atoms total_atoms6643
Residues n_residues807
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 dmax94.1
Rg (real space) rg_real29.81
Rg uncertainty (real space) rg_real_error0.42
I(0) (real space) i0_real1.4260e+08
I(0) uncertainty (real space) i0_real_error1.9180e+06
Rg (reciprocal space) rg_reciprocal29.84
I(0) (reciprocal space) i0_reciprocal142600000.0000
Solution quality estimate total_estimate0.9010
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary33.7
Skewness Skewness skewness0.290
Kurtosis Kurtosis kurtosis-0.496
Angular range angular_range— – 0.2650 −1
Current regularization parameter α current_alpha0.0002
Highest regularization parameter α highest_alpha44100000.0000
Real-space data points n_real_points54
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.918; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.953

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (8)

7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd4k5ka_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.174 — Nitric oxide (NO) synthase oxygenase domain
Superfamily Superfamily superfamilyd.174.1 — Nitric oxide (NO) synthase oxygenase domain
Family Family familyd.174.1.1 — Nitric oxide (NO) synthase oxygenase domain
Domain ID domain_idd4k5kb_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.174 — Nitric oxide (NO) synthase oxygenase domain
Superfamily Superfamily superfamilyd.174.1 — Nitric oxide (NO) synthase oxygenase domain
Family Family familyd.174.1.1 — Nitric oxide (NO) synthase oxygenase domain

CATH v4.4 (6 domains)

Domain ID domain_id4k5kA01
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology340 — Nitric Oxide Synthase; Chain A, domain 1
Homologous superfamily homologous superfamily10 — Nitric Oxide Synthase; Chain A, domain 1
Domain ID domain_id4k5kA02
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology440 — Nitric Oxide Synthase;Heme Domain; Chain A, domain 2
Homologous superfamily homologous superfamily10 — Nitric Oxide Synthase;Heme Domain;Chain A domain 2
Domain ID domain_id4k5kA03
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology1230 — Bovine Endothelial Nitric Oxide Synthase Heme Domain; Chain: A,domain 3
Homologous superfamily homologous superfamily10 — Nitric Oxide Synthase; Chain A, domain 3
Domain ID domain_id4k5kB01
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology340 — Nitric Oxide Synthase; Chain A, domain 1
Homologous superfamily homologous superfamily10 — Nitric Oxide Synthase; Chain A, domain 1
Domain ID domain_id4k5kB02
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology440 — Nitric Oxide Synthase;Heme Domain; Chain A, domain 2
Homologous superfamily homologous superfamily10 — Nitric Oxide Synthase;Heme Domain;Chain A domain 2
Domain ID domain_id4k5kB03
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology1230 — Bovine Endothelial Nitric Oxide Synthase Heme Domain; Chain: A,domain 3
Homologous superfamily homologous superfamily10 — Nitric Oxide Synthase; Chain A, domain 3

8. Citations (1)

9. Files and Curves (10)