5ago

Structure of rat neuronal nitric oxide synthase heme domain in complex with (S)-2-Amino-5-(2-mercaptoacetimidamido)pentanoic acid

Method: X-RAY DIFFRACTION Dmax: 94.7 Å Quality: EXCELLENT

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

NITRIC OXIDE SYNTHASE, BRAIN

RATTUS NORVEGICUS

UniProt P29476

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 297–718 Chain B; UniProt 297–718 Fragment:HEME DOMAIN, RESIDUES 297-718 HEM PROTOPORPHYRIN IX CONTAINING FE × 2 H4B 5,6,7,8-TETRAHYDROBIOPTERIN × 2 VUR (S)-2-AMINO-5-(2-MERCAPTOACETIMIDAMIDO)PENTANOIC ACID × 2 ACT ACETATE ION × 2 ZN ZINC ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:pH 5.8;20-22% PEG3350, 0.1M MES PH5.8, 140-200 MM AMMONIUM ACETATE, 10% ETHYLENE GLYCOL, 5 MM GSH, 30UM SDS Resolution 1.90 Å R-free 0.215

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.

348 other PDB entries and 351 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name NOS1_RAT
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–422; UniProt 297–718 Author chain B; PDBConstruct 1–422; UniProt 297–718

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 5ago

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id5ago
Deposition date deposition_date2015-02-02
Structure title titleStructure of rat neuronal nitric oxide synthase heme domain in complex with (S)-2-Amino-5-(2-mercaptoacetimidamido)pentanoic acid
Keywords keywordsOXIDOREDUCTASE, INHIBITOR COMPLEX; OXIDOREDUCTASE
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier30.08
Radius of gyration Rg (electron density) rg_electron29.39
Forward intensity I(0) i0146878000.00
Molecular weight molecular_weight96802.0 kDa
Excluded volume excluded_volume121130 ų
Envelope volume envelope_volume146530 ų
Hydration-shell volume shell_volume41002 ų
Envelope diameter envelope_diameter95.2
Shell Rg shell_rg37.43
Envelope Rg envelope_rg29.45
Shape Rg shape_rg29.41
Total Rg total_rg30.02
Total atoms total_atoms6814
Residues n_residues819
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 dmax94.7
Rg (real space) rg_real30.02
Rg uncertainty (real space) rg_real_error0.59
I(0) (real space) i0_real1.4690e+08
I(0) uncertainty (real space) i0_real_error1.8900e+06
Rg (reciprocal space) rg_reciprocal30.05
I(0) (reciprocal space) i0_reciprocal146900000.0000
Solution quality estimate total_estimate0.9005
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary34.0
Skewness Skewness skewness0.290
Kurtosis Kurtosis kurtosis-0.503
Angular range angular_range— – 0.2650 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha43400000.0000
Real-space data points n_real_points54
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.915; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.956

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (7)

7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd5agoa_
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_idd5agob_
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_id5agoA01
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_id5agoA02
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_id5agoA03
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_id5agoB01
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_id5agoB02
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_id5agoB03
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)