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- PDB-4d38: Structure of bovine endothelial nitric oxide synthase heme domain... -

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Basic information

Entry
Database: PDB / ID: 4d38
TitleStructure of bovine endothelial nitric oxide synthase heme domain in complex with (1R,2R)-2-(3-fluorobenzyl)-N-{2-[2-(1H-imidazol-1-yl)pyrimidin-4-yl]ethyl}cyclopropanamine
ComponentsNITRIC OXIDE SYNTHASE, ENDOTHELIAL
KeywordsOXIDOREDUCTASE / NITRIC OXIDE SYNTHASE / INHIBITOR COMPLEX
Function / homology
Function and homology information


cellular response to laminar fluid shear stress / negative regulation of leukocyte cell-cell adhesion / nitric oxide mediated signal transduction / nitric-oxide synthase (NADPH) / nitric-oxide synthase activity / L-arginine catabolic process / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / negative regulation of blood pressure / response to hormone / nitric oxide biosynthetic process ...cellular response to laminar fluid shear stress / negative regulation of leukocyte cell-cell adhesion / nitric oxide mediated signal transduction / nitric-oxide synthase (NADPH) / nitric-oxide synthase activity / L-arginine catabolic process / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / negative regulation of blood pressure / response to hormone / nitric oxide biosynthetic process / mitochondrion organization / caveola / blood coagulation / FMN binding / flavin adenine dinucleotide binding / NADP binding / response to lipopolysaccharide / cytoskeleton / calmodulin binding / 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, 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
ACETATE ION / 5,6,7,8-TETRAHYDROBIOPTERIN / PROTOPORPHYRIN IX CONTAINING FE / Chem-L5Z / Nitric oxide synthase 3
Similarity search - Component
Biological speciesBOS TAURUS (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 2.3 Å
AuthorsLi, H. / Poulos, T.L.
CitationJournal: J.Med.Chem. / Year: 2015
Title: Novel 2,4-Disubstituted Pyrimidines as Potent, Selective, and Cell-Permeable Inhibitors of Neuronal Nitric Oxide Synthase.
Authors: Mukherjee, P. / Li, H. / Sevrioukova, I. / Chreifi, G. / Martasek, P. / Roman, L.J. / Poulos, T.L. / Silverman, R.B.
History
DepositionOct 20, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 24, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 4, 2015Group: Database references
Revision 1.2Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_entry_details.has_protein_modification / _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_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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_conn_type.id / _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: NITRIC OXIDE SYNTHASE, ENDOTHELIAL
B: NITRIC OXIDE SYNTHASE, ENDOTHELIAL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,21213
Polymers99,4542
Non-polymers2,75811
Water4,486249
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10850 Å2
ΔGint-122 kcal/mol
Surface area32130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.870, 106.020, 156.340
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, ENDOTHELIAL / CONSTITUTIVE NOS / CNOS / EC-NOS / ENDOTHELIAL NOS / ENOS / NOS TYPE III / NOSIII / ENDOTHELIAL ...CONSTITUTIVE NOS / CNOS / EC-NOS / ENDOTHELIAL NOS / ENOS / NOS TYPE III / NOSIII / ENDOTHELIAL NITRIC OXIDE SYNTHASE


Mass: 49727.012 Da / Num. of mol.: 2 / Fragment: HEME DOMAIN, UNP RESIDUES 40-482
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BOS TAURUS (domestic cattle) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P29473, nitric-oxide synthase (NADPH)

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Non-polymers , 7 types, 260 molecules

#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


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


Mass: 241.247 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H15N5O3
#4: Chemical ChemComp-L5Z / (1R,2R)-2-(3-fluorobenzyl)-N-{2-[2-(1H-imidazol-1-yl)pyrimidin-4-yl]ethyl}cyclopropanamine


Mass: 337.394 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H20FN5
#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 249 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY
Sequence detailsRESIDUE 100 IS FOUND AS AN ARG IN STRUCTURE BUT IS A CYS IN DATABASE

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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: 2.5 Å3/Da / Density % sol: 50.7 % / Description: RMERGE 2.333 RPIM 1.763 CC ONE HALF 0.251
Crystal growpH: 6
Details: 20-22% PEG3350, 0.1 M CACODYLATE, 150-200 MM MG ACETATE, 5 MM TCEP, pH 6.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 20, 2014 / Details: MIRRORS
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 43431 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 4.9 % / Biso Wilson estimate: 48.56 Å2 / Rmerge(I) obs: 0.13 / Net I/σ(I): 7.7
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 4.9 % / Rmerge(I) obs: 1.5 / Mean I/σ(I) obs: 0.7 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
MOSFLMdata reduction
Aimlessdata scaling
REFMACphasing
RefinementMethod to determine structure: OTHER
Starting model: NONE

Resolution: 2.3→78.17 Å / SU ML: 0.39 / σ(F): 1.34 / Phase error: 26.65 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.23 2178 5 %
Rwork0.174 --
obs0.1768 43331 99.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.3→78.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6424 0 191 249 6864
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086819
X-RAY DIFFRACTIONf_angle_d1.1539311
X-RAY DIFFRACTIONf_dihedral_angle_d16.0072453
X-RAY DIFFRACTIONf_chiral_restr0.073972
X-RAY DIFFRACTIONf_plane_restr0.0051197
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.35010.36811400.35122506X-RAY DIFFRACTION99
2.3501-2.40470.39781400.32492551X-RAY DIFFRACTION100
2.4047-2.46490.37351400.30972536X-RAY DIFFRACTION100
2.4649-2.53150.38011490.29022534X-RAY DIFFRACTION100
2.5315-2.6060.35911470.28252519X-RAY DIFFRACTION100
2.606-2.69010.29231290.24132566X-RAY DIFFRACTION100
2.6901-2.78630.31321270.22622565X-RAY DIFFRACTION100
2.7863-2.89790.2641110.21082585X-RAY DIFFRACTION100
2.8979-3.02970.24431430.19092573X-RAY DIFFRACTION100
3.0297-3.18950.27031360.18542548X-RAY DIFFRACTION100
3.1895-3.38930.25481320.18352563X-RAY DIFFRACTION99
3.3893-3.6510.2131330.1532586X-RAY DIFFRACTION99
3.651-4.01840.1911290.13992571X-RAY DIFFRACTION99
4.0184-4.59980.16621460.12122592X-RAY DIFFRACTION99
4.5998-5.7950.19841180.12962650X-RAY DIFFRACTION99
5.795-78.21510.18461580.15252708X-RAY DIFFRACTION98
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.0215-0.5073-0.61221.31050.45131.682-0.0058-0.00160.0233-0.21950.0881-0.1632-0.09360.094-0.07060.3468-0.06160.02350.2741-0.01250.305411.098510.317531.7522
20.713-0.43950.52231.5031-0.87682.78680.0571-0.1034-0.03820.07020.0410.00740.0145-0.0304-0.07520.3091-0.03370.00740.33770.00230.31992.65725.78767.6065
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 67:482)
2X-RAY DIFFRACTION2(CHAIN B AND RESID 69:482)

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