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- PDB-4uh5: Structure of human nNOS R354A G357D mutant heme domain in complex... -

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Basic information

Entry
Database: PDB / ID: 4uh5
TitleStructure of human nNOS R354A G357D mutant heme domain in complex with N1-(5-(2-(6-Amino-4-methylpyridin-2-yl)ethyl)pyridin-3-yl)-N1,N2- dimethylethane-1,2-diamine
ComponentsNEURONAL NITRIC OXIDE SYNTHASE
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 / tetrahydrobiopterin binding / arginine binding / regulation of cardiac muscle contraction by calcium ion signaling / regulation of calcium ion transmembrane transport via high voltage-gated calcium channel / synaptic signaling by nitric oxide ...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 / tetrahydrobiopterin binding / arginine binding / regulation of cardiac muscle contraction by calcium ion signaling / regulation of calcium ion transmembrane transport via high voltage-gated calcium channel / synaptic signaling by nitric oxide / positive regulation of adenylate cyclase-activating G protein-coupled receptor signaling pathway / positive regulation of sodium ion transmembrane transport / peptidyl-cysteine S-nitrosylase activity / positive regulation of the force of heart contraction / cadmium ion binding / negative regulation of calcium ion transport / negative regulation of potassium ion transport / regulation of postsynaptic membrane potential / nitric oxide mediated signal transduction / sodium channel regulator activity / nitric-oxide synthase (NADPH) / regulation of neurogenesis / regulation of cardiac muscle contraction / negative regulation of serotonin uptake / nitric-oxide synthase activity / multicellular organismal response to stress / xenobiotic catabolic process / L-arginine catabolic process / striated muscle contraction / negative regulation of blood pressure / regulation of sodium ion transport / Ion homeostasis / response to hormone / photoreceptor inner segment / nitric oxide biosynthetic process / T-tubule / sarcoplasmic reticulum membrane / cell redox homeostasis / calyx of Held / sarcoplasmic reticulum / cell periphery / calcium channel regulator activity / establishment of localization in cell / sarcolemma / caveola / potassium ion transport / cellular response to growth factor stimulus / vasodilation / Z disc / calcium-dependent protein binding / calcium ion transport / FMN binding / NADP binding / flavin adenine dinucleotide binding / positive regulation of neuron apoptotic process / response to heat / scaffold protein binding / response to lipopolysaccharide / dendritic spine / transmembrane transporter binding / calmodulin binding / response to hypoxia / cytoskeleton / postsynaptic density / 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 / PDZ 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 / 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
Chem-EXI / 5,6,7,8-TETRAHYDROBIOPTERIN / PROTOPORPHYRIN IX CONTAINING FE / Nitric oxide synthase 1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.983 Å
AuthorsLi, H. / Poulos, T.L.
CitationJournal: J.Med.Chem. / Year: 2015
Title: 2-Aminopyridines with a Truncated Side Chain to Improve Human Neuronal Nitric Oxide Synthase Inhibitory Potency and Selectivity.
Authors: Kang, S. / Li, H. / Tang, W. / Martasek, P. / Roman, L.J. / Poulos, T.L. / Silverman, R.B.
History
DepositionMar 23, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 15, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 5, 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: NEURONAL NITRIC OXIDE SYNTHASE
B: NEURONAL NITRIC OXIDE SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,02011
Polymers97,5692
Non-polymers2,4519
Water5,350297
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9780 Å2
ΔGint-112.7 kcal/mol
Surface area33820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.420, 122.570, 164.010
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 NEURONAL NITRIC OXIDE SYNTHASE


Mass: 48784.496 Da / Num. of mol.: 2 / Mutation: YES [R354A G357D]
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 , 6 types, 306 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-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-EXI / N1-(5-(2-(6-Amino-4-methylpyridin-2-yl)ethyl)pyridin-3-yl)-N1,N2-dimethylethane-1,2-diamine


Mass: 299.414 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H25N5
#6: Chemical ChemComp-ZN / ZINC ION


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


Mass: 18.015 Da / Num. of mol.: 297 / 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: 2.74 Å3/Da / Density % sol: 55.2 % / Description: RMERGE 1.710 RPIM 1.555 CC ONE HALF 0.335
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: SSRL / Beamline: BL14-1 / Wavelength: 1.127
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Dec 16, 2014 / Details: MIRROR
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.127 Å / Relative weight: 1
ReflectionResolution: 1.98→50 Å / Num. obs: 71749 / % possible obs: 97 % / Observed criterion σ(I): -3 / Redundancy: 3.9 % / Biso Wilson estimate: 37 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 5.3
Reflection shellResolution: 1.98→2.05 Å / Redundancy: 3.6 % / Rmerge(I) obs: 1.5 / Mean I/σ(I) obs: 0.4 / % possible all: 90.1

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
MOSFLMdata reduction
Aimlessdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.983→39.835 Å / SU ML: 0.35 / σ(F): 0.53 / Phase error: 31.63 / Stereochemistry target values: ML
Details: RESIDUES 344 TO 348 IN CHAIN A AND 344 TO 353 IN CHAIN B ARE DISORDERED
RfactorNum. reflection% reflection
Rfree0.2469 6722 4.9 %
Rwork0.195 --
obs0.1975 71655 96.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.983→39.835 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6720 0 167 297 7184
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0077120
X-RAY DIFFRACTIONf_angle_d1.1519693
X-RAY DIFFRACTIONf_dihedral_angle_d15.3862597
X-RAY DIFFRACTIONf_chiral_restr0.071000
X-RAY DIFFRACTIONf_plane_restr0.0051228
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.983-2.00550.39062470.40844014X-RAY DIFFRACTION90
2.0055-2.02910.43681970.39844099X-RAY DIFFRACTION91
2.0291-2.05390.40572040.38464096X-RAY DIFFRACTION91
2.0539-2.07990.43292040.37524133X-RAY DIFFRACTION92
2.0799-2.10720.3982250.36814145X-RAY DIFFRACTION93
2.1072-2.13610.39282580.35074207X-RAY DIFFRACTION95
2.1361-2.16660.40051750.33164315X-RAY DIFFRACTION96
2.1666-2.1990.34322270.31684323X-RAY DIFFRACTION96
2.199-2.23330.36342190.30074380X-RAY DIFFRACTION97
2.2333-2.26990.35132010.30394433X-RAY DIFFRACTION97
2.2699-2.30910.31472220.2834228X-RAY DIFFRACTION96
2.3091-2.3510.32612260.25624392X-RAY DIFFRACTION98
2.351-2.39630.3082550.25014397X-RAY DIFFRACTION98
2.3963-2.44520.30072350.25664340X-RAY DIFFRACTION98
2.4452-2.49830.3152670.24554426X-RAY DIFFRACTION98
2.4983-2.55640.2722200.22314360X-RAY DIFFRACTION98
2.5564-2.62030.28012250.22194412X-RAY DIFFRACTION98
2.6203-2.69120.30822730.22744331X-RAY DIFFRACTION98
2.6912-2.77040.25731790.21934524X-RAY DIFFRACTION98
2.7704-2.85970.26382150.19994380X-RAY DIFFRACTION98
2.8597-2.96190.28322220.19844416X-RAY DIFFRACTION99
2.9619-3.08050.24732300.1954443X-RAY DIFFRACTION99
3.0805-3.22060.24262220.20244414X-RAY DIFFRACTION99
3.2206-3.39030.26332110.18474441X-RAY DIFFRACTION99
3.3903-3.60260.21372380.15994444X-RAY DIFFRACTION99
3.6026-3.88060.19192420.14914413X-RAY DIFFRACTION99
3.8806-4.27070.20712430.13384479X-RAY DIFFRACTION99
4.2707-4.88770.16222230.12794476X-RAY DIFFRACTION99
4.8877-6.15430.20932170.15254463X-RAY DIFFRACTION99
6.1543-39.84350.18232000.15164472X-RAY DIFFRACTION99
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)
11.0372-0.3178-0.20551.30280.26293.68850.0007-0.03810.0126-0.0647-0.0811-0.04640.21010.180.06910.1988-0.02630.02870.28790.04450.2647117.7416250.1745358.5381
20.9317-0.169-0.41951.12160.34915.32640.03960.1834-0.04-0.1255-0.1090.11670.056-0.35220.04580.28670.01350.00730.3734-0.03660.2873116.33248.8934321.445
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 302:721)
2X-RAY DIFFRACTION2(CHAIN B AND RESID 304:721)

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