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- PDB-8skn: Crystal structure of compound 3-bound human Dynamin-1-like protei... -

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Basic information

Entry
Database: PDB / ID: 8skn
TitleCrystal structure of compound 3-bound human Dynamin-1-like protein GTPase-BSE fusion
ComponentsDynamin-1-like protein GTPase-BSE fusion
KeywordsHYDROLASE/INHIBITOR / inhibitor / HYDROLASE-INHIBITOR complex
Function / homology
Function and homology information


GTPase activity / GTP binding
Similarity search - Function
Dynamin GTPase effector / Dynamin GTPase effector domain / Dynamin GTPase effector domain / Dynamin, GTPase region, conserved site / Dynamin-type guanine nucleotide-binding (G) domain signature. / Dynamin stalk domain / Dynamin central region / GTPase effector domain / GED domain profile. / Dynamin, GTPase domain ...Dynamin GTPase effector / Dynamin GTPase effector domain / Dynamin GTPase effector domain / Dynamin, GTPase region, conserved site / Dynamin-type guanine nucleotide-binding (G) domain signature. / Dynamin stalk domain / Dynamin central region / GTPase effector domain / GED domain profile. / Dynamin, GTPase domain / Dynamin, GTPase / Dynamin / Dynamin-type guanine nucleotide-binding (G) domain / Dynamin-type guanine nucleotide-binding (G) domain profile. / Dynamin, N-terminal / Dynamin family / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Chem-6I9 / Dynamin 1-like, isoform CRA_a
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.41 Å
AuthorsMa, B.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Acs Med.Chem.Lett. / Year: 2023
Title: Discovery of Potent Allosteric DRP1 Inhibitors by Disrupting Protein-Protein Interaction with MiD49.
Authors: Furuya, T. / Lin, J. / Afanaseva, A. / Molz, L. / Lagu, B. / Ma, B.
History
DepositionApr 20, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 30, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Dynamin-1-like protein GTPase-BSE fusion
B: Dynamin-1-like protein GTPase-BSE fusion
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,16214
Polymers85,1192
Non-polymers1,04212
Water2,846158
1
A: Dynamin-1-like protein GTPase-BSE fusion
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,3549
Polymers42,5601
Non-polymers7948
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Dynamin-1-like protein GTPase-BSE fusion
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,8085
Polymers42,5601
Non-polymers2484
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.580, 81.270, 97.080
Angle α, β, γ (deg.)90.00, 101.19, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Dynamin-1-like protein GTPase-BSE fusion


Mass: 42559.660 Da / Num. of mol.: 2 / Fragment: UNP residues 54-382,725-752
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DNM1L, hCG_1810949 / Production host: Escherichia coli (E. coli) / References: UniProt: D3DUW7, Hydrolases
#2: Chemical ChemComp-6I9 / N-[4-(azetidin-1-yl)-2-(4-methylphenyl)quinolin-6-yl]-2-methylpropanamide


Mass: 359.464 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H25N3O / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 158 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.16 Å3/Da / Density % sol: 43.14 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.05 M potassium chloride, 0.01 M magnesium chloride, 15% w/v PEG6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97843 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 2, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97843 Å / Relative weight: 1
ReflectionResolution: 2.41→47.66 Å / Num. obs: 28133 / % possible obs: 99.8 % / Redundancy: 6.8 % / CC1/2: 0.994 / Rmerge(I) obs: 0.175 / Rpim(I) all: 0.072 / Rrim(I) all: 0.189 / Χ2: 1 / Net I/σ(I): 10.2
Reflection shellResolution: 2.41→2.5 Å / % possible obs: 99.9 % / Redundancy: 7 % / Rmerge(I) obs: 0.966 / Num. measured all: 20605 / Num. unique obs: 2955 / CC1/2: 0.735 / Rpim(I) all: 0.391 / Rrim(I) all: 1.043 / Χ2: 1 / Net I/σ(I) obs: 2.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4H1V

4h1v


Resolution: 2.41→47.66 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.896 / SU B: 9.431 / SU ML: 0.214 / Cross valid method: THROUGHOUT / ESU R: 0.543 / ESU R Free: 0.284 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25555 1438 5.1 %RANDOM
Rwork0.20563 ---
obs0.20819 26672 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 43.259 Å2
Baniso -1Baniso -2Baniso -3
1--0.98 Å2-0 Å20.45 Å2
2---0.73 Å2-0 Å2
3---1.42 Å2
Refinement stepCycle: 1 / Resolution: 2.41→47.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5255 0 71 158 5484
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0135382
X-RAY DIFFRACTIONr_bond_other_d0.0010.0155471
X-RAY DIFFRACTIONr_angle_refined_deg1.3861.6527254
X-RAY DIFFRACTIONr_angle_other_deg1.1681.58812563
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6015663
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.63622.036275
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.837151016
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5281545
X-RAY DIFFRACTIONr_chiral_restr0.0640.2731
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025922
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021145
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_it3.094.3872676
X-RAY DIFFRACTIONr_mcbond_other3.094.3872675
X-RAY DIFFRACTIONr_mcangle_it4.9786.5513331
X-RAY DIFFRACTIONr_mcangle_other4.9776.5513332
X-RAY DIFFRACTIONr_scbond_it3.1484.7882706
X-RAY DIFFRACTIONr_scbond_other3.1484.7882707
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.116.9863922
X-RAY DIFFRACTIONr_long_range_B_refined7.6751.0535728
X-RAY DIFFRACTIONr_long_range_B_other7.65851.0625699
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 9715 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.11 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.41→2.473 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.314 108 -
Rwork0.264 1956 -
obs--99.76 %

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