5fvz

Structure of bovine endothelial nitric oxide synthase heme domain in complex with 6-(2-(5-(3-(dimethylamino)propyl)pyridin-3-yl)ethyl)-4-methylpyridin-2-amine

Method: X-RAY DIFFRACTION Dmax: 94.6 Å Quality: REASONABLE

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

ENDOTHELIAL NITRIC OXIDE SYNTHASE

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, 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 W67 6-(2-(5-(3-(DIMETHYLAMINO)PROPYL)PYRIDIN-3-YL)ETHYL)-4-METHYLPYRIDIN-2-AMINE × 2 GOL GLYCEROL × 2 ZN ZINC ION × 1 CL CHLORIDE ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions:pH 6;20-22% PEG3350 0.1M CACODYLATE, PH6.0 140-200 MM MG ACETATE 5 MM TCEP Resolution 2.05 Å R-free 0.211

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 5fvz

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id5fvz
Deposition date deposition_date2016-02-10
Structure title titleStructure of bovine endothelial nitric oxide synthase heme domain in complex with 6-(2-(5-(3-(dimethylamino)propyl)pyridin-3-yl)ethyl)-4-methylpyridin-2-amine
Keywords keywordsOXIDOREDUCTASE, NITRIC OXIDE SYNTHASE, INHIBITOR COMPLEX; OXIDOREDUCTASE
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier30.04
Radius of gyration Rg (electron density) rg_electron29.16
Forward intensity I(0) i0141559000.00
Molecular weight molecular_weight93997.0 kDa
Excluded volume excluded_volume117270 ų
Envelope volume envelope_volume143070 ų
Hydration-shell volume shell_volume40412 ų
Envelope diameter envelope_diameter94.4
Shell Rg shell_rg37.03
Envelope Rg envelope_rg29.26
Shape Rg shape_rg29.17
Total Rg total_rg29.79
Total atoms total_atoms6616
Residues n_residues806
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 dmax94.6
Rg (real space) rg_real29.98
Rg uncertainty (real space) rg_real_error0.43
I(0) (real space) i0_real1.4160e+08
I(0) uncertainty (real space) i0_real_error1.9360e+06
Rg (reciprocal space) rg_reciprocal30.01
I(0) (reciprocal space) i0_reciprocal141600000.0000
Solution quality estimate total_estimate0.6816
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks0
Primary peak position r_peak_primary
Skewness Skewness skewness0.290
Kurtosis Kurtosis kurtosis-0.493
Angular range angular_range— – 0.2650 −1
Current regularization parameter α current_alpha0.0001
Highest regularization parameter α highest_alpha43120000.0000
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: 0.050; Positv: 1.000; Valcen: 1.000; Smooth: 0.952

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_idd5fvza_
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_idd5fvzb_
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_id5fvzA01
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_id5fvzA02
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_id5fvzA03
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_id5fvzB01
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_id5fvzB02
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_id5fvzB03
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)