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- PDB-8bi9: Structure of a cyclic beta-hairpin peptide derived from neuronal ... -

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Basic information

Entry
Database: PDB / ID: 8bi9
TitleStructure of a cyclic beta-hairpin peptide derived from neuronal nitric oxide synthase (T112W/T116E variant)
ComponentsNitric oxide synthase, brain
KeywordsPROTEIN BINDING / cyclic beta-hairpin / neuronal nitric oxidase synthase / inhibitor of the NOS/PSD-95 interaction / peptide drugs / stroke treatment
Function / homology
Function and homology information


negative regulation of calcium ion transport into cytosol / myoblast fusion / Nitric oxide stimulates guanylate cyclase / ROS and RNS production in phagocytes / negative regulation of hydrolase activity / tetrahydrobiopterin binding / arginine binding / regulation of calcium ion transmembrane transport via high voltage-gated calcium channel / retrograde trans-synaptic signaling by nitric oxide / positive regulation of sodium ion transmembrane transport ...negative regulation of calcium ion transport into cytosol / myoblast fusion / Nitric oxide stimulates guanylate cyclase / ROS and RNS production in phagocytes / negative regulation of hydrolase activity / tetrahydrobiopterin binding / arginine binding / regulation of calcium ion transmembrane transport via high voltage-gated calcium channel / retrograde trans-synaptic signaling by nitric oxide / positive regulation of sodium ion transmembrane transport / positive regulation of adenylate cyclase-activating G protein-coupled receptor signaling pathway / peptidyl-cysteine S-nitrosylation / cadmium ion binding / positive regulation of the force of heart contraction / negative regulation of potassium ion transport / negative regulation of calcium ion transport / negative regulation of serotonin uptake / sodium channel regulator activity / striated muscle contraction / nitric-oxide synthase (NADPH) / regulation of cardiac muscle contraction / multicellular organismal response to stress / xenobiotic catabolic process / nitric-oxide synthase activity / nitric oxide mediated signal transduction / arginine catabolic process / regulation of sodium ion transport / regulation of ryanodine-sensitive calcium-release channel activity / Ion homeostasis / photoreceptor inner segment / nitric oxide biosynthetic process / negative regulation of blood pressure / response to hormone / cell redox homeostasis / sarcoplasmic reticulum / muscle contraction / cell periphery / sarcolemma / cellular response to growth factor stimulus / vasodilation / calcium-dependent protein binding / FMN binding / flavin adenine dinucleotide binding / positive regulation of peptidyl-serine phosphorylation / NADP binding / response to heat / scaffold protein binding / transmembrane transporter binding / response to lipopolysaccharide / dendritic spine / postsynaptic density / response to hypoxia / cytoskeleton / calmodulin binding / membrane raft / synapse / heme binding / perinuclear region of cytoplasm / positive regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / protein-containing complex / mitochondrion / nucleoplasm / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
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 ...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 / PDZ domain / Flavoprotein-like superfamily / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily
Similarity search - Domain/homology
TERTIARY-BUTYL ALCOHOL / Nitric oxide synthase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.44 Å
AuthorsBalboa, J.R. / Ostergaard, S. / Stromgaard, K. / Knapp, S. / Joerger, A.C. / Structural Genomics Consortium (SGC)
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)JO 1473/1-3 Germany
CitationJournal: J.Med.Chem. / Year: 2023
Title: Development of a Potent Cyclic Peptide Inhibitor of the nNOS/PSD-95 Interaction.
Authors: Balboa, J.R. / Essig, D.J. / Ma, S. / Karer, N. / Clemmensen, L.S. / Pedersen, S.W. / Joerger, A.C. / Knapp, S. / Ostergaard, S. / Stromgaard, K.
History
DepositionNov 1, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 21, 2022Provider: repository / Type: Initial release
Revision 1.1Jul 5, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Nitric oxide synthase, brain
A: Nitric oxide synthase, brain
C: Nitric oxide synthase, brain
D: Nitric oxide synthase, brain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,4815
Polymers10,4074
Non-polymers741
Water1,42379
1
B: Nitric oxide synthase, brain


Theoretical massNumber of molelcules
Total (without water)2,6021
Polymers2,6021
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Nitric oxide synthase, brain


Theoretical massNumber of molelcules
Total (without water)2,6021
Polymers2,6021
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Nitric oxide synthase, brain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,6762
Polymers2,6021
Non-polymers741
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Nitric oxide synthase, brain


Theoretical massNumber of molelcules
Total (without water)2,6021
Polymers2,6021
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.739, 29.872, 58.940
Angle α, β, γ (deg.)90.000, 108.593, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11D-1206-

HOH

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Components

#1: Protein/peptide
Nitric oxide synthase, brain / / Constitutive NOS / NC-NOS / NOS type I / Neuronal NOS / N-NOS / nNOS / Peptidyl-cysteine S- ...Constitutive NOS / NC-NOS / NOS type I / Neuronal NOS / N-NOS / nNOS / Peptidyl-cysteine S-nitrosylase NOS1 / bNOS


Mass: 2601.842 Da / Num. of mol.: 4 / Source method: obtained synthetically / Details: cyclic peptide / Source: (synth.) Homo sapiens (human) / References: UniProt: P29475, nitric-oxide synthase (NADPH)
#2: Chemical ChemComp-TBU / TERTIARY-BUTYL ALCOHOL / 2-METHYL-2-PROPANOL / Tert-Butyl alcohol


Mass: 74.122 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 79 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 1.71 Å3/Da / Density % sol: 28.21 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 16% (v/v) tert-butanol, 0.1 M sodium citrate pH 3.9

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 16, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.44→27.93 Å / Num. obs: 11979 / % possible obs: 93.2 % / Redundancy: 3.6 % / Biso Wilson estimate: 14.1403650487 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.03 / Net I/σ(I): 26.2
Reflection shellResolution: 1.44→1.46 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.077 / Mean I/σ(I) obs: 10.8 / Num. unique obs: 1176 / CC1/2: 0.99 / % possible all: 62.8

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1QAV

1qav


Resolution: 1.44→24.04 Å / SU ML: 0.128584547618 / Cross valid method: FREE R-VALUE / σ(F): 1.47833559702 / Phase error: 23.2379736273
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.183407647785 677 5.65391681978 %
Rwork0.151544646339 11297 -
obs0.153394317432 11974 92.5490802288 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 17.9827115008 Å2
Refinement stepCycle: LAST / Resolution: 1.44→24.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms717 0 5 79 801
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00486271908691773
X-RAY DIFFRACTIONf_angle_d0.8623558517521067
X-RAY DIFFRACTIONf_chiral_restr0.0703022326438117
X-RAY DIFFRACTIONf_plane_restr0.00577064021995141
X-RAY DIFFRACTIONf_dihedral_angle_d21.5219790826273
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.44-1.55120.2350421874851130.1402635836981869X-RAY DIFFRACTION78.031496063
1.5512-1.70720.2214603469661570.1407206428622308X-RAY DIFFRACTION95.9143968872
1.7072-1.95420.1903979606391410.1233171593422320X-RAY DIFFRACTION95.6842923795
1.9542-2.46170.1817142776491320.1591237255822401X-RAY DIFFRACTION97.686077902
2.4617-24.040.1676117073561340.1601927051612399X-RAY DIFFRACTION95.1182876455

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