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- PDB-2hx2: Bovine eNOS heme domain complexed with (4S)-N-{4-Amino-5-[(2-amin... -

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Basic information

Entry
Database: PDB / ID: 2hx2
TitleBovine eNOS heme domain complexed with (4S)-N-{4-Amino-5-[(2-aminoethyl)-hydroxyamino]-pentyl}-N'-nitroguanidine
ComponentsNitric-oxide synthaseNitric oxide synthase
KeywordsOXIDOREDUCTASE / nitric oxide synthase / heme enzyme / inhibitor
Function / homology
Function and homology information


cellular response to laminar fluid shear stress / positive regulation of guanylate cyclase activity / negative regulation of leukocyte cell-cell adhesion / nitric-oxide synthase (NADPH) / nitric-oxide synthase activity / nitric oxide mediated signal transduction / arginine catabolic process / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / mitochondrion organization / negative regulation of blood pressure ...cellular response to laminar fluid shear stress / positive regulation of guanylate cyclase activity / negative regulation of leukocyte cell-cell adhesion / nitric-oxide synthase (NADPH) / nitric-oxide synthase activity / nitric oxide mediated signal transduction / arginine catabolic process / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / mitochondrion organization / negative regulation of blood pressure / nitric oxide biosynthetic process / response to hormone / caveola / blood coagulation / FMN binding / flavin adenine dinucleotide binding / NADP binding / response to lipopolysaccharide / calmodulin binding / cytoskeleton / heme binding / Golgi apparatus / metal ion binding / nucleus / plasma membrane / cytosol
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, domain 2 superfamily / Nitric oxide synthase, domain 1 superfamily / Nitric oxide synthase, domain 3 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, domain 2 superfamily / Nitric oxide synthase, domain 1 superfamily / Nitric oxide synthase, domain 3 superfamily / Nitric oxide synthase, N-terminal / Nitric oxide synthase, N-terminal domain 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-3HX / ACETATE ION / CACODYLATE ION / 5,6,7,8-TETRAHYDROBIOPTERIN / PROTOPORPHYRIN IX CONTAINING FE / Nitric oxide synthase 3
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.95 Å
AuthorsIgarashi, J. / Li, H. / Poulos, T.L.
Citation
Journal: J.Med.Chem. / Year: 2007
Title: Structure-Based Design and Synthesis of N(omega)-Nitro-l-Arginine-Containing Peptidomimetics as Selective Inhibitors of Neuronal Nitric Oxide Synthase. Displacement of the Heme Structural Water.
Authors: Seo, J. / Igarashi, J. / Li, H. / Martasek, P. / Roman, L.J. / Poulos, T.L. / Silverman, R.B.
#1: Journal: Nat.Struct.Mol.Biol. / Year: 2004
Title: Structural basis for dipeptide amide isoform-selective inhibition of neuronal nitric oxide synthase
Authors: Flinspach, M. / Li, H. / Jamal, J. / Yang, W. / Huang, H. / Hah, J.M. / Gomez-Vidal, A. / Litzinger, E.A. / Silverman, R.B. / Poulos, T.L.
History
DepositionAug 2, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 24, 2007Provider: repository / Type: Initial release
Revision 1.1Apr 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999SEQUENCE Authors state that residue at position 100 is an Arg as supported by observed electron density

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Nitric-oxide synthase
B: Nitric-oxide synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,71017
Polymers93,7082
Non-polymers3,00215
Water9,674537
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12720 Å2
ΔGint-77 kcal/mol
Surface area31650 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)57.820, 106.850, 156.350
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Nitric-oxide synthase / Nitric oxide synthase / EC-NOS / NOS type III / NOSIII / Endothelial NOS / eNOS / Constitutive NOS / cNOS


Mass: 46854.027 Da / Num. of mol.: 2 / Fragment: residues 66-481
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Gene: NOS3 / Plasmid: pCWori / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P29473, nitric-oxide synthase (NADPH)

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Non-polymers , 8 types, 552 molecules

#2: Chemical ChemComp-CAC / CACODYLATE ION / dimethylarsinate / Cacodylic acid


Mass: 136.989 Da / Num. of mol.: 2 / Fragment: residues 66-481 / Source method: obtained synthetically / Formula: C2H6AsO2 / References: nitric-oxide synthase (NADPH)
#3: Chemical
ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#6: Chemical ChemComp-H4B / 5,6,7,8-TETRAHYDROBIOPTERIN / Tetrahydrobiopterin


Mass: 241.247 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H15N5O3 / Comment: neurotransmitter*YM
#7: Chemical ChemComp-3HX / (4S)-N-{4-AMINO-5-[(2-AMINOETHYL)(HYDROXYAMINO]-PENTYL}-N'-NITROGUANIDINE


Mass: 263.297 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H21N7O3
#8: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 537 / Source method: isolated from a natural source / Formula: H2O

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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: 2.58 Å3/Da / Density % sol: 52.24 %
Crystal growTemperature: 280 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: PEG3350, cacodylate Mg acetate, TCEP, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 280K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL1-5 / Wavelength: 0.9998 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 18, 2005 / Details: mirrors
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9998 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. obs: 69992 / % possible obs: 98.5 % / Observed criterion σ(I): -3 / Redundancy: 3.9 % / Biso Wilson estimate: 20.6 Å2 / Rmerge(I) obs: 0.052 / Rsym value: 0.052 / Net I/σ(I): 10.2
Reflection shellResolution: 1.95→1.98 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.558 / Mean I/σ(I) obs: 2.2 / Rsym value: 0.558 / % possible all: 97.1

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.95→48.36 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 2473448.95 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.213 3472 5 %RANDOM
Rwork0.18 ---
obs0.18 69931 98.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 48.4827 Å2 / ksol: 0.373458 e/Å3
Displacement parametersBiso mean: 34.3 Å2
Baniso -1Baniso -2Baniso -3
1-5.14 Å20 Å20 Å2
2---0.51 Å20 Å2
3----4.64 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.24 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.23 Å0.19 Å
Refinement stepCycle: LAST / Resolution: 1.95→48.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6404 0 191 537 7132
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.6
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.03
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 1.95→2.07 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.289 542 4.9 %
Rwork0.241 10455 -
obs--93.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2hetero.parhetero.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION43hx.par3hx.top

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