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- PDB-2wyz: L38V SOD1 mutant complexed with UMP -

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Basic information

Entry
Database: PDB / ID: 2wyz
TitleL38V SOD1 mutant complexed with UMP
ComponentsSUPEROXIDE DISMUTASE [CU-ZN]
KeywordsOXIDOREDUCTASE / DISEASE MUTATION / AMYOTROPHIC LATERAL SCLEROSIS / ANTIOXIDANT
Function / homology
Function and homology information


action potential initiation / response to antipsychotic drug / neurofilament cytoskeleton organization / response to carbon monoxide / protein phosphatase 2B binding / dense core granule / relaxation of vascular associated smooth muscle / anterograde axonal transport / regulation of organ growth / response to superoxide ...action potential initiation / response to antipsychotic drug / neurofilament cytoskeleton organization / response to carbon monoxide / protein phosphatase 2B binding / dense core granule / relaxation of vascular associated smooth muscle / anterograde axonal transport / regulation of organ growth / response to superoxide / regulation of T cell differentiation in thymus / positive regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / peripheral nervous system myelin maintenance / retina homeostasis / auditory receptor cell stereocilium organization / hydrogen peroxide biosynthetic process / cellular response to potassium ion / retrograde axonal transport / superoxide anion generation / regulation of GTPase activity / myeloid cell homeostasis / response to copper ion / superoxide metabolic process / muscle cell cellular homeostasis / superoxide dismutase / heart contraction / Detoxification of Reactive Oxygen Species / superoxide dismutase activity / cellular response to ATP / cellular response to cadmium ion / transmission of nerve impulse / negative regulation of reproductive process / negative regulation of developmental process / regulation of multicellular organism growth / ectopic germ cell programmed cell death / response to axon injury / neuronal action potential / ovarian follicle development / positive regulation of superoxide anion generation / axon cytoplasm / glutathione metabolic process / embryo implantation / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / dendrite cytoplasm / removal of superoxide radicals / reactive oxygen species metabolic process / positive regulation of phagocytosis / response to amphetamine / thymus development / placenta development / positive regulation of cytokine production / determination of adult lifespan / regulation of mitochondrial membrane potential / response to nutrient levels / locomotory behavior / response to hydrogen peroxide / sensory perception of sound / mitochondrial intermembrane space / small GTPase binding / negative regulation of inflammatory response / regulation of blood pressure / peroxisome / Platelet degranulation / protein-folding chaperone binding / response to heat / cytoplasmic vesicle / response to ethanol / spermatogenesis / gene expression / negative regulation of neuron apoptotic process / intracellular iron ion homeostasis / lysosome / positive regulation of MAPK cascade / positive regulation of apoptotic process / mitochondrial matrix / response to xenobiotic stimulus / copper ion binding / neuronal cell body / apoptotic process / protein homodimerization activity / protein-containing complex / mitochondrion / extracellular space / extracellular exosome / extracellular region / zinc ion binding / nucleoplasm / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Superoxide dismutase, copper/zinc binding domain / Copper/Zinc superoxide dismutase signature 1. / Superoxide dismutase (Cu/Zn) / superoxide dismutase copper chaperone / Superoxide dismutase, copper/zinc, binding site / Copper/Zinc superoxide dismutase signature 2. / Superoxide dismutase, copper/zinc binding domain / Copper/zinc superoxide dismutase (SODC) / Superoxide dismutase-like, copper/zinc binding domain superfamily / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
COPPER (II) ION / URIDINE-5'-MONOPHOSPHATE / Superoxide dismutase [Cu-Zn]
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsAntonyuk, S.V. / Strange, R.W. / Hasnain, S.S.
CitationJournal: J.Med.Chem. / Year: 2010
Title: Structural Discovery of Small Molecule Binding Sites in Cu-Zn Human Superoxide Dismutase Familial Amyotrophic Lateral Sclerosis Mutants Provides Insights for Lead Optimization.
Authors: Antonyuk, S.V. / Strange, R.W. / Hasnain, S.S.
History
DepositionNov 20, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 27, 2010Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 12, 2017Group: Derived calculations
Category: pdbx_struct_conn_angle / struct_conn / struct_conn_type
Item: _struct_conn_type.id
Revision 1.4Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / 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 / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_PDB_ins_code / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_PDB_ins_code / _struct_conn.pdbx_ptnr2_label_alt_id / _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_ins_code / _struct_site.pdbx_auth_seq_id
Revision 1.5Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SUPEROXIDE DISMUTASE [CU-ZN]
F: SUPEROXIDE DISMUTASE [CU-ZN]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,75613
Polymers31,6592
Non-polymers1,09711
Water7,026390
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2890 Å2
ΔGint-178.9 kcal/mol
Surface area13840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.717, 67.589, 50.777
Angle α, β, γ (deg.)90.00, 105.98, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AF

#1: Protein SUPEROXIDE DISMUTASE [CU-ZN]


Mass: 15829.533 Da / Num. of mol.: 2 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P00441, superoxide dismutase

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Non-polymers , 5 types, 401 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-U5P / URIDINE-5'-MONOPHOSPHATE


Mass: 324.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H13N2O9P
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 390 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsENGINEERED RESIDUE IN CHAIN A, LEU 39 TO VAL ENGINEERED RESIDUE IN CHAIN F, LEU 39 TO VAL
Has protein modificationY

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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: 2.1 Å3/Da / Density % sol: 40 % / Description: NONE
Crystal growpH: 7.5
Details: 150 MM NACL, 3.0 M AMMONIUM SULPHATE, 100 MM TRIS PH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX10.1 / Wavelength: 0.98
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 24, 2006 / Details: MIRRORS
RadiationMonochromator: SI111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.7→24 Å / Num. obs: 26774 / % possible obs: 96.9 % / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 14.8 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 11
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 2 / % possible all: 69.9

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Processing

Software
NameVersionClassification
REFMAC5.5.0106refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2C9V

2c9v


Resolution: 1.7→24 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.913 / SU B: 2.755 / SU ML: 0.092 / Cross valid method: THROUGHOUT / ESU R: 0.134 / ESU R Free: 0.138 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.23934 1340 5 %RANDOM
Rwork0.1756 ---
obs0.17893 25327 96.18 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 11.723 Å2
Baniso -1Baniso -2Baniso -3
1-0.6 Å20 Å2-0.03 Å2
2---0.29 Å2-0 Å2
3----0.33 Å2
Refinement stepCycle: LAST / Resolution: 1.7→24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2220 0 47 390 2657
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0212375
X-RAY DIFFRACTIONr_bond_other_d0.0010.021564
X-RAY DIFFRACTIONr_angle_refined_deg1.4851.9633229
X-RAY DIFFRACTIONr_angle_other_deg0.8833865
X-RAY DIFFRACTIONr_dihedral_angle_1_deg12.5165.122329
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.58225.545101
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.15615390
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.78159
X-RAY DIFFRACTIONr_chiral_restr0.0890.2354
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022719
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02429
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9121.51523
X-RAY DIFFRACTIONr_mcbond_other0.261.5661
X-RAY DIFFRACTIONr_mcangle_it1.54722438
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.1883852
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.3824.5780
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.313 60 -
Rwork0.287 1325 -
obs--67.89 %

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