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- PDB-4nos: HUMAN INDUCIBLE NITRIC OXIDE SYNTHASE WITH INHIBITOR -

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Basic information

Entry
Database: PDB / ID: 4nos
TitleHUMAN INDUCIBLE NITRIC OXIDE SYNTHASE WITH INHIBITOR
ComponentsINDUCIBLE NITRIC OXIDE SYNTHASE
KeywordsOXIDOREDUCTASE / L-ARGININE MONOOXYGENASE / NITRIC OXIDE / HUMAN / ZNS4
Function / homology
Function and homology information


positive regulation of leukocyte mediated cytotoxicity / Inhibition of nitric oxide production / peptidyl-cysteine S-nitrosylation / regulation of cellular respiration / Nitric oxide stimulates guanylate cyclase / prostaglandin secretion / ROS and RNS production in phagocytes / tetrahydrobiopterin binding / arginine binding / superoxide metabolic process ...positive regulation of leukocyte mediated cytotoxicity / Inhibition of nitric oxide production / peptidyl-cysteine S-nitrosylation / regulation of cellular respiration / Nitric oxide stimulates guanylate cyclase / prostaglandin secretion / ROS and RNS production in phagocytes / tetrahydrobiopterin binding / arginine binding / superoxide metabolic process / cortical cytoskeleton / regulation of cytokine production involved in inflammatory response / Fc-gamma receptor signaling pathway involved in phagocytosis / peroxisomal matrix / nitric oxide mediated signal transduction / nitric-oxide synthase (NADPH) / nitric-oxide synthase activity / L-arginine catabolic process / negative regulation of blood pressure / response to hormone / nitric oxide biosynthetic process / regulation of insulin secretion / innate immune response in mucosa / cell redox homeostasis / positive regulation of interleukin-8 production / response to bacterium / Peroxisomal protein import / negative regulation of protein catabolic process / cellular response to type II interferon / positive regulation of interleukin-6 production / circadian rhythm / peroxisome / FMN binding / cellular response to xenobiotic stimulus / flavin adenine dinucleotide binding / NADP binding / regulation of cell population proliferation / cellular response to lipopolysaccharide / defense response to Gram-negative bacterium / Interleukin-4 and Interleukin-13 signaling / response to lipopolysaccharide / response to hypoxia / calmodulin binding / defense response to bacterium / inflammatory response / negative regulation of gene expression / heme binding / perinuclear region of cytoplasm / protein homodimerization activity / nucleoplasm / metal ion binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Bovine Endothelial Nitric Oxide Synthase Heme Domain; Chain: A,domain 3 / Nitric Oxide Synthase; Chain A, domain 3 / Nitric Oxide Synthase; Chain A, domain 1 / Nitric Oxide Synthase; Chain A, domain 1 / Nitric Oxide Synthase;Heme Domain; Chain A, domain 2 / Nitric Oxide Synthase;Heme Domain;Chain A domain 2 / Nitric-oxide synthase, eukaryote / Nitric oxide synthase, N-terminal / Nitric oxide synthase, N-terminal domain superfamily / Nitric oxide synthase, domain 2 superfamily ...Bovine Endothelial Nitric Oxide Synthase Heme Domain; Chain: A,domain 3 / Nitric Oxide Synthase; Chain A, domain 3 / Nitric Oxide Synthase; Chain A, domain 1 / Nitric Oxide Synthase; Chain A, domain 1 / Nitric Oxide Synthase;Heme Domain; Chain A, domain 2 / Nitric Oxide Synthase;Heme Domain;Chain A domain 2 / Nitric-oxide synthase, eukaryote / Nitric oxide synthase, N-terminal / Nitric oxide synthase, N-terminal domain superfamily / Nitric oxide synthase, domain 2 superfamily / Nitric oxide synthase, domain 1 superfamily / Nitric oxide synthase, domain 3 superfamily / : / Nitric oxide synthase, oxygenase domain / Nitric oxide synthase (NOS) signature. / Sulfite reductase [NADPH] flavoprotein alpha-component-like, FAD-binding / NADPH-cytochrome p450 reductase, FAD-binding, alpha-helical domain superfamily / FAD binding domain / Flavodoxin-like / Flavoprotein pyridine nucleotide cytochrome reductase / Flavodoxin / Flavodoxin-like domain profile. / Flavodoxin/nitric oxide synthase / Oxidoreductase FAD/NAD(P)-binding / Oxidoreductase NAD-binding domain / FAD-binding domain, ferredoxin reductase-type / Ferredoxin-NADP reductase (FNR), nucleotide-binding domain / Ferredoxin reductase-type FAD binding domain profile. / Riboflavin synthase-like beta-barrel / Flavoprotein-like superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Chem-H2B / 5,6,7,8-TETRAHYDROBIOPTERIN / PROTOPORPHYRIN IX CONTAINING FE / ETHYLISOTHIOUREA / Nitric oxide synthase, inducible
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 2.25 Å
AuthorsFischmann, T.O. / Weber, P.C.
CitationJournal: Nat.Struct.Biol. / Year: 1999
Title: Structural characterization of nitric oxide synthase isoforms reveals striking active-site conservation.
Authors: Fischmann, T.O. / Hruza, A. / Niu, X.D. / Fossetta, J.D. / Lunn, C.A. / Dolphin, E. / Prongay, A.J. / Reichert, P. / Lundell, D.J. / Narula, S.K. / Weber, P.C.
History
DepositionFeb 3, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Feb 4, 2000Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: INDUCIBLE NITRIC OXIDE SYNTHASE
B: INDUCIBLE NITRIC OXIDE SYNTHASE
C: INDUCIBLE NITRIC OXIDE SYNTHASE
D: INDUCIBLE NITRIC OXIDE SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)201,82218
Polymers197,8454
Non-polymers3,97614
Water24,6991371
1
A: INDUCIBLE NITRIC OXIDE SYNTHASE
B: INDUCIBLE NITRIC OXIDE SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,9109
Polymers98,9232
Non-polymers1,9877
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10030 Å2
ΔGint-114 kcal/mol
Surface area32100 Å2
MethodPISA, PQS
2
C: INDUCIBLE NITRIC OXIDE SYNTHASE
D: INDUCIBLE NITRIC OXIDE SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,9129
Polymers98,9232
Non-polymers1,9897
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9930 Å2
ΔGint-114 kcal/mol
Surface area32360 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)89.759, 156.672, 190.044
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.9927, 0.10291, 0.06293), (0.11374, 0.62488, 0.77239), (0.04016, 0.77391, -0.63202)22.00306, 22.59963, -50.29379
2given(0.99998, 0.00358, -0.00451), (-0.00054, 0.83766, 0.5462), (0.00573, -0.54619, 0.83764)-1.40336, 52.21081, 8.07962
3given(-0.99189, 0.05568, 0.11429), (0.1191, 0.0926, 0.98855), (0.04446, 0.99415, -0.09848)28.94339, 61.45053, -15.62112

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
INDUCIBLE NITRIC OXIDE SYNTHASE / INOS / NOS2


Mass: 49461.367 Da / Num. of mol.: 4 / Fragment: OXYGENASE DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PINOS60-3 / Production host: Escherichia coli (E. coli) / References: UniProt: P35228, nitric-oxide synthase (NADPH)

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Non-polymers , 6 types, 1385 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#4: Chemical ChemComp-H2B / 2-AMINO-6-(1,2-DIHYDROXY-PROPYL)-7,8-DIHYDRO-6H-PTERIDIN-4-ONE / QUINONOID 7,8-TETRAHYDROBIOPTERIN


Mass: 239.231 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H13N5O3
#5: Chemical
ChemComp-ITU / ETHYLISOTHIOUREA


Mass: 104.174 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8N2S
#6: Chemical ChemComp-H4B / 5,6,7,8-TETRAHYDROBIOPTERIN


Mass: 241.247 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C9H15N5O3 / Comment: neurotransmitter*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1371 / Source method: isolated from a natural source / Formula: H2O

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Details

Nonpolymer detailsHIGH-SPIN STATE ZNS4 CLUSTER LOCATED AT THE DIMER INTERFACE

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.38 Å3/Da / Density % sol: 63.56 %
Crystal growpH: 6.9 / Details: pH 6.90
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
130 mg/mlprotein1drop
250 mMMES1reservoir
31.6 M1reservoirMgSO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1.2
DetectorType: SIEMENS / Detector: CCD / Date: Dec 1, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2 Å / Relative weight: 1
ReflectionResolution: 2.25→18.8 Å / Num. obs: 113089 / % possible obs: 89.2 % / Observed criterion σ(I): -3 / Redundancy: 2.4 % / Biso Wilson estimate: 29 Å2 / Rsym value: 0.057 / Net I/σ(I): 10.2
Reflection shellResolution: 2.25→2.29 Å / Redundancy: 1.7 % / Mean I/σ(I) obs: 3.2 / Rsym value: 0.23 / % possible all: 80.7
Reflection
*PLUS
Rmerge(I) obs: 0.057
Reflection shell
*PLUS
% possible obs: 80.7 % / Rmerge(I) obs: 0.23

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Processing

Software
NameVersionClassification
SHARPphasing
SOLOMONphasing
X-PLOR3.1refinement
DENZOdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MIRAS / Resolution: 2.25→8 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 0 / Data cutoff low absF: 0 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.289 5550 5 %RANDOM
Rwork0.199 ---
obs-109101 88.7 %-
Displacement parametersBiso mean: 28 Å2
Refinement stepCycle: LAST / Resolution: 2.25→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13680 0 266 1371 15317
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.011
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.63
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Refine LS restraints NCSNCS model details: RESTRAINTS
LS refinement shellResolution: 2.25→2.33 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.34 490 5 %
Rwork0.3 9281 -
obs--80.3 %

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