1vaf

Inducible nitric oxide synthase oxygenase domain complexed with the inhibitor AR-R17477

Method: X-RAY DIFFRACTION Dmax: 122.3 Å Quality: REASONABLE

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

Nitric oxide synthase, inducible

Mus musculus

UniProt P29477

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 77–495 Fragment:Inducible Nitric Oxide Synthase Oxygenase Domain (residues 77-495) ZN ZINC ION × 2 HEM PROTOPORPHYRIN IX CONTAINING FE × 2 H4B 5,6,7,8-TETRAHYDROBIOPTERIN × 2 ARR N-(4-{2-[(3-CHLOROBENZYL)AMINO]ETHYL}PHENYL)THIOPHENE-2-CARBOXIMIDAMIDE × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7;277 K;MES, SODIUM-MALONATE, EPPS, NACL, GLYCEROL, H4B, beta-MERCAPTOETHANOL, AR-R17477, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K Resolution 2.90 Å R-free 0.262
2 Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain B; UniProt 77–495 Fragment:Inducible Nitric Oxide Synthase Oxygenase Domain (residues 77-495) ZN ZINC ION × 2 HEM PROTOPORPHYRIN IX CONTAINING FE × 2 H4B 5,6,7,8-TETRAHYDROBIOPTERIN × 2 ARR N-(4-{2-[(3-CHLOROBENZYL)AMINO]ETHYL}PHENYL)THIOPHENE-2-CARBOXIMIDAMIDE × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7;277 K;MES, SODIUM-MALONATE, EPPS, NACL, GLYCEROL, H4B, beta-MERCAPTOETHANOL, AR-R17477, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K Resolution 2.90 Å R-free 0.262

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.

50 other PDB entries and 90 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name NOS2_MOUSE
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–419; UniProt 77–495 Author chain B; PDBConstruct 1–419; UniProt 77–495

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 1vaf

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1vaf
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1vaf
Deposition date deposition_date2004-02-16
Structure title titleInducible nitric oxide synthase oxygenase domain complexed with the inhibitor AR-R17477
Keywords keywordsMURINE INOSOXY INHIBITOR COMPLEX, OXIDOREDUCTASE; OXIDOREDUCTASE
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier37.64
Radius of gyration Rg (electron density) rg_electron37.40
Forward intensity I(0) i0148280000.00
Molecular weight molecular_weight99419.0 kDa
Excluded volume excluded_volume124440 ų
Envelope volume envelope_volume161670 ų
Hydration-shell volume shell_volume36479 ų
Envelope diameter envelope_diameter123.9
Shell Rg shell_rg42.60
Envelope Rg envelope_rg36.95
Shape Rg shape_rg37.38
Total Rg total_rg37.81
Total atoms total_atoms7002
Residues n_residues838
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 dmax122.3
Rg (real space) rg_real38.94
Rg uncertainty (real space) rg_real_error0.42
I(0) (real space) i0_real1.4720e+08
I(0) uncertainty (real space) i0_real_error2.1890e+06
Rg (reciprocal space) rg_reciprocal37.72
I(0) (reciprocal space) i0_reciprocal148300000.0000
Solution quality estimate total_estimate0.6460
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary29.1
Skewness Skewness skewness0.379
Kurtosis Kurtosis kurtosis-0.693
Angular range angular_range— – 0.2100 −1
Current regularization parameter α current_alpha3.1240
Highest regularization parameter α highest_alpha22590000.0000
Real-space data points n_real_points43
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.813; Stabil: 0.928; Sysdev: 0.000; Positv: 1.000; Valcen: 0.819; Smooth: 0.387

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (6)

7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd1vafa_
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_idd1vafb_
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_id1vafA01
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_id1vafA02
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_id1vafA03
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_id1vafB01
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_id1vafB02
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_id1vafB03
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)