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- PDB-5adi: Structure of human nNOS R354A G357D mutant heme domain in complex... -

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Basic information

Entry
Database: PDB / ID: 5adi
TitleStructure of human nNOS R354A G357D mutant heme domain in complex with 7-(((5-((Methylamino)methyl)pyridin-3-yl)oxy)methyl)quinolin-2- amine
ComponentsNITRIC OXIDE SYNTHASE, BRAIN
KeywordsOXIDOREDUCTASE / NITRIC OXIDE SYNTHASE
Function / homology
Function and homology information


positive regulation of membrane repolarization during ventricular cardiac muscle cell action potential / negative regulation of calcium ion transport into cytosol / Nitric oxide stimulates guanylate cyclase / myoblast fusion / ROS and RNS production in phagocytes / negative regulation of hydrolase activity / tetrahydrobiopterin binding / regulation of cardiac muscle contraction by calcium ion signaling / arginine binding / regulation of calcium ion transmembrane transport via high voltage-gated calcium channel ...positive regulation of membrane repolarization during ventricular cardiac muscle cell action potential / negative regulation of calcium ion transport into cytosol / Nitric oxide stimulates guanylate cyclase / myoblast fusion / ROS and RNS production in phagocytes / negative regulation of hydrolase activity / tetrahydrobiopterin binding / regulation of cardiac muscle contraction by calcium ion signaling / arginine binding / regulation of calcium ion transmembrane transport via high voltage-gated calcium channel / 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 / regulation of cardiac muscle contraction / negative regulation of serotonin uptake / calcium channel regulator activity / nitric-oxide synthase (NADPH) / multicellular organismal response to stress / regulation of ryanodine-sensitive calcium-release channel activity / sodium channel regulator activity / nitric oxide mediated signal transduction / nitric-oxide synthase activity / xenobiotic catabolic process / arginine catabolic process / striated muscle contraction / regulation of sodium ion transport / Ion homeostasis / nitric oxide biosynthetic process / negative regulation of blood pressure / photoreceptor inner segment / response to hormone / cell redox homeostasis / sarcoplasmic reticulum / cell periphery / cellular response to growth factor stimulus / sarcolemma / vasodilation / calcium-dependent protein binding / FMN binding / positive regulation of peptidyl-serine phosphorylation / flavin adenine dinucleotide binding / NADP binding / response to heat / scaffold protein binding / transmembrane transporter binding / response to lipopolysaccharide / dendritic spine / postsynaptic density / cytoskeleton / response to hypoxia / calmodulin binding / membrane raft / heme binding / synapse / positive regulation of DNA-templated transcription / perinuclear region of cytoplasm / positive regulation of transcription by RNA polymerase II / protein-containing complex / mitochondrion / nucleoplasm / 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 / PDZ domain / Flavoprotein-like superfamily / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
5,6,7,8-TETRAHYDROBIOPTERIN / PROTOPORPHYRIN IX CONTAINING FE / Chem-TUE / Nitric oxide synthase 1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsLi, H. / Poulos, T.L.
CitationJournal: J.Med.Chem. / Year: 2015
Title: Phenyl Ether- and Aniline-Containing 2-Aminoquinolines as Potent and Selective Inhibitors of Neuronal Nitric Oxide Synthase.
Authors: Cinelli, M.A. / Li, H. / Pensa, A.V. / Kang, S. / Roman, L.J. / Martasek, P. / Poulos, T.L. / Silverman, R.B.
History
DepositionAug 20, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 28, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 25, 2015Group: Database references
Revision 1.2May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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_database_status.status_code_sf / _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.pdbx_dist_value / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NITRIC OXIDE SYNTHASE, BRAIN
B: NITRIC OXIDE SYNTHASE, BRAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,22710
Polymers97,5692
Non-polymers2,6588
Water7,080393
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9320 Å2
ΔGint-85.5 kcal/mol
Surface area33550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.210, 122.800, 164.400
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, 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 / NEURONAL NITRIC OXIDE SYNTHASE


Mass: 48784.496 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 302-721 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P29475

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Non-polymers , 5 types, 401 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-TUE / 7-[[5-[(methylideneamino)methyl]pyridin-3-yl]oxymethyl]quinolin-2-amine


Mass: 292.335 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C17H16N4O
#5: Chemical ChemComp-ZN / ZINC ION


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


Mass: 18.015 Da / Num. of mol.: 393 / 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: 2.69 Å3/Da / Density % sol: 54 %
Description: OVERALL RMERGE 0.132 RPIM 0.099 CC ONE HALF 0.989 HIGHEST RESOLUTION SHELL RMERGE 1.695 RPIM 1.298 CC ONE HALF 0.301
Crystal growpH: 6.2
Details: 8-9% PED3350 40MM CITRIC ACID 60MM BISTRISPROPANE 10% GLYCEROL 5MM TCEP, pH 6.2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 9, 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: 2.2→50 Å / Num. obs: 54717 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 4.9 % / Biso Wilson estimate: 36.98 Å2 / Rmerge(I) obs: 0.13 / Net I/σ(I): 8.1
Reflection shellResolution: 2.2→2.3 Å / Redundancy: 5 % / Rmerge(I) obs: 1.5 / Mean I/σ(I) obs: 0.9 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
MOSFLMdata reduction
Aimlessdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→68.309 Å / SU ML: 0.31 / σ(F): 0 / Phase error: 26.72 / Stereochemistry target values: ML
Details: RESIDUES 344 TO 351 IN CHAIN A AND 344 TO 353 IN CHAIN B ARE DISORDERED
RfactorNum. reflection% reflection
Rfree0.2368 5063 4.9 %
Rwork0.1846 --
obs0.1872 54597 99.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.2→68.309 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6693 0 187 393 7273
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0077114
X-RAY DIFFRACTIONf_angle_d1.1359684
X-RAY DIFFRACTIONf_dihedral_angle_d15.1632581
X-RAY DIFFRACTIONf_chiral_restr0.071996
X-RAY DIFFRACTIONf_plane_restr0.0051221
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.2250.41211610.35073303X-RAY DIFFRACTION100
2.225-2.25120.41941780.36263269X-RAY DIFFRACTION99
2.2512-2.27870.40351440.34413328X-RAY DIFFRACTION100
2.2787-2.30750.36441760.33713253X-RAY DIFFRACTION100
2.3075-2.33790.34331550.30833286X-RAY DIFFRACTION100
2.3379-2.36990.32151880.29943302X-RAY DIFFRACTION100
2.3699-2.40380.3591970.28813223X-RAY DIFFRACTION100
2.4038-2.43960.32291740.28713253X-RAY DIFFRACTION100
2.4396-2.47780.35661910.28433309X-RAY DIFFRACTION100
2.4778-2.51840.32381810.26193221X-RAY DIFFRACTION100
2.5184-2.56180.26761690.25353300X-RAY DIFFRACTION100
2.5618-2.60840.31281580.23813340X-RAY DIFFRACTION100
2.6084-2.65860.30571990.24563201X-RAY DIFFRACTION100
2.6586-2.71280.28541740.24443240X-RAY DIFFRACTION99
2.7128-2.77180.30711400.22913354X-RAY DIFFRACTION100
2.7718-2.83630.29351550.22633285X-RAY DIFFRACTION100
2.8363-2.90720.28261520.21033326X-RAY DIFFRACTION100
2.9072-2.98580.25741780.19323255X-RAY DIFFRACTION100
2.9858-3.07370.21981640.18673309X-RAY DIFFRACTION100
3.0737-3.17290.23981490.17833268X-RAY DIFFRACTION100
3.1729-3.28630.23411650.17463310X-RAY DIFFRACTION100
3.2863-3.41790.22831700.16983281X-RAY DIFFRACTION100
3.4179-3.57340.19381790.14983236X-RAY DIFFRACTION100
3.5734-3.76180.19341850.13723300X-RAY DIFFRACTION100
3.7618-3.99750.18541790.13323276X-RAY DIFFRACTION100
3.9975-4.30610.20051670.12653300X-RAY DIFFRACTION100
4.3061-4.73930.15631730.11993302X-RAY DIFFRACTION100
4.7393-5.42490.18881630.13413241X-RAY DIFFRACTION100
5.4249-6.83380.20571640.15753299X-RAY DIFFRACTION100
6.8338-68.34180.20041350.16063305X-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)
10.5137-0.16690.12560.93290.23981.77480.010.00880.025-0.0604-0.0526-0.05310.06560.17090.03760.1502-0.0170.04510.21790.04480.2341117.2316250.4667359.1951
20.3943-0.2758-0.01720.76640.03472.89980.00550.0498-0.02270.0166-0.07440.08960.04-0.06920.06550.1992-0.01960.03820.2468-0.03220.2594115.7749249.3145322.0441
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 302:721)
2X-RAY DIFFRACTION2(CHAIN B AND RESID 302:721)

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