4d1p

Structure of human endothelial nitric oxide synthase heme domain IN COMPLEX WITH 6-((((3S, 5R)-5-(((6-AMINO-4-METHYLPYRIDIN-2-YL)METHOXY) METHYL)PYRROLIDIN-3-YL)OXY) METHYL)-4-METHYLPYRIDIN-2-AMINE

Method: X-RAY DIFFRACTION Dmax: 94.3 Å Quality: EXCELLENT

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

NITRIC OXIDE SYNTHASE, ENDOTHELIAL

HOMO SAPIENS

UniProt P29474

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 41–480 Chain B; UniProt 41–480 Not recorded HEM PROTOPORPHYRIN IX CONTAINING FE × 2 H4B 5,6,7,8-TETRAHYDROBIOPTERIN × 2 Q16 6-((((3S, 5R)-5-(((6-amino-4-methylpyridin-2-yl)methoxy)methyl)pyrrolidin-3-yl)oxy)methyl)-4-methylpyridin-2-amine × 2 ACT ACETATE ION × 4 BTB 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 4 GOL GLYCEROL × 1 ZN ZINC ION × 1 GD GADOLINIUM ATOM × 2 X-RAY DIFFRACTION X-ray crystallization conditions:pH 7.5;10-12% PEG3350 0.1M BIS TRIS, PH7.5 0.3M MG ACETATE, 0.1M GDCL3, 5 MM TCEP Resolution 1.73 Å R-free 0.186

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.

94 other PDB entries and 183 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name NOS3_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–440; UniProt 41–480 Author chain B; PDBConstruct 1–440; UniProt 41–480

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 4d1p

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 4d1p
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2. Structure Basics 2. Structure Basics

Entry ID entry_id4d1p
Deposition date deposition_date2014-05-02
Structure title titleStructure of human endothelial nitric oxide synthase heme domain IN COMPLEX WITH 6-((((3S, 5R)-5-(((6-AMINO-4-METHYLPYRIDIN-2-YL)METHOXY) METHYL)PYRROLIDIN-3-YL)OXY) METHYL)-4-METHYLPYRIDIN-2-AMINE
Keywords keywordsOXIDOREDUCTASE, NITRIC OXIDE SYNTHASE; OXIDOREDUCTASE
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier30.18
Radius of gyration Rg (electron density) rg_electron29.32
Forward intensity I(0) i0143937000.00
Molecular weight molecular_weight94774.0 kDa
Excluded volume excluded_volume118080 ų
Envelope volume envelope_volume142210 ų
Hydration-shell volume shell_volume40067 ų
Envelope diameter envelope_diameter96.9
Shell Rg shell_rg37.10
Envelope Rg envelope_rg29.43
Shape Rg shape_rg29.29
Total Rg total_rg30.06
Total atoms total_atoms6662
Residues n_residues803
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 dmax94.3
Rg (real space) rg_real30.12
Rg uncertainty (real space) rg_real_error0.43
I(0) (real space) i0_real1.4390e+08
I(0) uncertainty (real space) i0_real_error2.1490e+06
Rg (reciprocal space) rg_reciprocal30.15
I(0) (reciprocal space) i0_reciprocal143900000.0000
Solution quality estimate total_estimate0.9022
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary35.6
Skewness Skewness skewness0.288
Kurtosis Kurtosis kurtosis-0.505
Angular range angular_range— – 0.2650 −1
Current regularization parameter α current_alpha0.0008
Highest regularization parameter α highest_alpha43590000.0000
Real-space data points n_real_points54
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.930; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.935

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (10)

7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd4d1pa_
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_idd4d1pb_
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_id4d1pA01
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_id4d1pA02
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_id4d1pA03
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_id4d1pB01
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_id4d1pB02
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_id4d1pB03
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)