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- PDB-4d39: Structure of bovine endothelial nitric oxide synthase heme domain... -

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Basic information

Entry
Database: PDB / ID: 4d39
TitleStructure of bovine endothelial nitric oxide synthase heme domain in complex with2-(2-(1H-imidazol-1-yl)pyrimidin-4-yl)-N-(3-cyanobenzyl) ethan-1-amine
ComponentsNITRIC OXIDE SYNTHASE, ENDOTHELIAL
KeywordsOXIDOREDUCTASE / NITRIC OXIDE SYNTHASE / INHIBITOR COMPLEX
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 mediated signal transduction / nitric-oxide synthase activity / arginine catabolic process / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / nitric oxide biosynthetic process / 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 mediated signal transduction / nitric-oxide synthase activity / arginine catabolic process / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / nitric oxide biosynthetic process / negative regulation of blood pressure / response to hormone / mitochondrion organization / caveola / blood coagulation / FMN binding / flavin adenine dinucleotide binding / NADP binding / response to lipopolysaccharide / cytoskeleton / calmodulin binding / heme binding / Golgi apparatus / nucleus / metal ion binding / 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 / D-MANNITOL / Chem-OLW / Nitric oxide synthase 3
Similarity search - Component
Biological speciesBOS TAURUS (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 2 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 1.2Oct 23, 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)102,51015
Polymers99,4542
Non-polymers3,05613
Water8,989499
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11660 Å2
ΔGint-115.2 kcal/mol
Surface area32080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.756, 106.122, 156.308
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 (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 , 8 types, 512 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 / Comment: neurotransmitter*YM
#4: Chemical ChemComp-OLW / 3-[({2-[2-(1H-imidazol-1-yl)pyrimidin-4-yl]ethyl}amino)methyl]benzonitrile / 2-[2-(1H-imidazol-1-yl)pyrimidin-4-yl]-N-(3-cyanobenzyl)ethan-1-amine


Mass: 304.349 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H16N6
#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#6: Chemical ChemComp-MTL / D-MANNITOL


Mass: 182.172 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O6 / Comment: medication*YM
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


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


Mass: 18.015 Da / Num. of mol.: 499 / 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 2.221 RPIM 1.052 CC ONE HALF 0.222
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: SSRL / Beamline: BL14-1 / Wavelength: 1.127
DetectorType: MARRESEARCH / Detector: CCD / Date: Jul 29, 2014 / Details: MIRRORS
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.127 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 65857 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 5.1 % / Biso Wilson estimate: 36.79 Å2 / Rmerge(I) obs: 0.13 / Net I/σ(I): 8.2
Reflection shellResolution: 2→2.05 Å / Redundancy: 5 % / Rmerge(I) obs: 1.5 / Mean I/σ(I) obs: 0.7 / % possible all: 95.8

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Processing

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

Resolution: 2→39.077 Å / SU ML: 0.31 / σ(F): 1.19 / Phase error: 24.78 / Stereochemistry target values: ML
Details: RESIDUES 110 TO 120 IN BOTH CHAIN A AND CHAIN B ARE DISORDERED.
RfactorNum. reflection% reflection
Rfree0.222 6270 5 %
Rwork0.1722 --
obs0.1747 65523 99.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→39.077 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6444 0 211 499 7154
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086862
X-RAY DIFFRACTIONf_angle_d1.1549366
X-RAY DIFFRACTIONf_dihedral_angle_d15.9082474
X-RAY DIFFRACTIONf_chiral_restr0.071979
X-RAY DIFFRACTIONf_plane_restr0.0051203
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.02270.36092210.35433803X-RAY DIFFRACTION98
2.0227-2.04650.3742360.35793953X-RAY DIFFRACTION98
2.0465-2.07150.36931650.32933922X-RAY DIFFRACTION98
2.0715-2.09770.37682230.3273906X-RAY DIFFRACTION100
2.0977-2.12530.35652330.31383983X-RAY DIFFRACTION99
2.1253-2.15440.31632060.29953890X-RAY DIFFRACTION99
2.1544-2.18520.33771890.28983971X-RAY DIFFRACTION100
2.1852-2.21780.33292200.28553969X-RAY DIFFRACTION99
2.2178-2.25250.32212080.27813928X-RAY DIFFRACTION99
2.2525-2.28940.28931850.26273990X-RAY DIFFRACTION100
2.2894-2.32890.28371920.24813970X-RAY DIFFRACTION99
2.3289-2.37120.28592300.24443927X-RAY DIFFRACTION100
2.3712-2.41680.28881950.23074026X-RAY DIFFRACTION100
2.4168-2.46610.28452260.22623932X-RAY DIFFRACTION100
2.4661-2.51970.29122340.21763960X-RAY DIFFRACTION100
2.5197-2.57830.24162330.20243864X-RAY DIFFRACTION100
2.5783-2.64280.22122070.18973999X-RAY DIFFRACTION100
2.6428-2.71420.24532020.18043950X-RAY DIFFRACTION100
2.7142-2.79410.26242070.17993993X-RAY DIFFRACTION100
2.7941-2.88420.21491700.17344021X-RAY DIFFRACTION100
2.8842-2.98730.23222070.16353949X-RAY DIFFRACTION100
2.9873-3.10690.19762230.15623939X-RAY DIFFRACTION100
3.1069-3.24820.23392070.16343976X-RAY DIFFRACTION100
3.2482-3.41930.20762040.14663983X-RAY DIFFRACTION100
3.4193-3.63340.17052060.13363944X-RAY DIFFRACTION100
3.6334-3.91370.20572130.13173934X-RAY DIFFRACTION100
3.9137-4.30710.16761940.12083978X-RAY DIFFRACTION100
4.3071-4.92930.14572000.11363984X-RAY DIFFRACTION100
4.9293-6.20640.20192020.13373966X-RAY DIFFRACTION100
6.2064-39.08440.17412320.14193943X-RAY DIFFRACTION100
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)
10.9614-0.35-0.57981.41460.42851.50490.0026-0.01530.0262-0.16610.0806-0.1895-0.02750.114-0.08050.2585-0.03780.00160.2243-0.00880.249611.176810.326931.7984
20.9037-0.39720.42051.3898-1.05812.37090.0217-0.0995-0.03650.11090.05520.0067-0.0184-0.035-0.06510.2417-0.0143-0.0050.2338-0.01320.23582.80995.991667.572
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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