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- PDB-5mim: Xray structure of human furin bound with the 2,5-dideoxystreptami... -

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Basic information

Entry
Database: PDB / ID: 5mim
TitleXray structure of human furin bound with the 2,5-dideoxystreptamine derived small molecule inhibitor 1n
ComponentsFurin
KeywordsHYDROLASE / proprotein convertase / inhibitor / protease / complex
Function / homology
Function and homology information


Signaling by PDGF / Amyloid fiber formation / Assembly of active LPL and LIPC lipase complexes / Formation of the cornified envelope / Uptake and function of anthrax toxins / TGF-beta receptor signaling activates SMADs / Signaling by NODAL / Pre-NOTCH Processing in Golgi / Synthesis and processing of ENV and VPU / NGF processing ...Signaling by PDGF / Amyloid fiber formation / Assembly of active LPL and LIPC lipase complexes / Formation of the cornified envelope / Uptake and function of anthrax toxins / TGF-beta receptor signaling activates SMADs / Signaling by NODAL / Pre-NOTCH Processing in Golgi / Synthesis and processing of ENV and VPU / NGF processing / Removal of aminoterminal propeptides from gamma-carboxylated proteins / Activation of Matrix Metalloproteinases / Elastic fibre formation / Collagen degradation / zymogen inhibition / positive regulation of transforming growth factor beta1 activation / dibasic protein processing / furin / nerve growth factor production / regulation of lipoprotein lipase activity / nerve growth factor processing / regulation of low-density lipoprotein particle receptor biosynthetic process / negative regulation of low-density lipoprotein particle receptor catabolic process / signal peptide processing / negative regulation of transforming growth factor beta1 production / peptide biosynthetic process / peptide hormone processing / secretion by cell / integral component of Golgi membrane / nerve growth factor binding / cornification / trans-Golgi network transport vesicle / regulation of endopeptidase activity / zymogen activation / positive regulation of membrane protein ectodomain proteolysis / regulation of protein catabolic process / regulation of signal transduction / protein processing / collagen catabolic process / extracellular matrix disassembly / peptide binding / viral protein processing / trans-Golgi network / viral life cycle / serine-type endopeptidase inhibitor activity / transforming growth factor beta receptor signaling pathway / Golgi lumen / extracellular matrix organization / peptidase activity / endopeptidase activity / endosome membrane / protease binding / membrane raft / Golgi membrane / serine-type endopeptidase activity / cellular protein metabolic process / endoplasmic reticulum / cell surface / extracellular exosome / membrane / extracellular region / plasma membrane / metal ion binding
Peptidase S8, subtilisin-related / Proprotein convertase P-domain / Serine proteases, subtilase family, serine active site. / Serine proteases, subtilase family, histidine active site. / Serine proteases, subtilase family, aspartic acid active site. / Furin-like repeat / P domain / Peptidase S8 pro-domain / Peptidase S8, subtilisin, His-active site / P/Homo B domain profile. ...Peptidase S8, subtilisin-related / Proprotein convertase P-domain / Serine proteases, subtilase family, serine active site. / Serine proteases, subtilase family, histidine active site. / Serine proteases, subtilase family, aspartic acid active site. / Furin-like repeat / P domain / Peptidase S8 pro-domain / Peptidase S8, subtilisin, His-active site / P/Homo B domain profile. / Peptidase S8/S53 domain / Peptidase S8, subtilisin, Asp-active site / Subtilase family / Peptidase S8, pro-domain superfamily / Peptidase S8, subtilisin, Ser-active site / Peptidase S8/S53 domain superfamily / Peptidase S8, pro-domain / Galactose-binding-like domain superfamily / Serine proteases, subtilase domain profile. / Growth factor receptor cysteine-rich domain superfamily / Kexin/furin catalytic domain
Furin
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsDahms, S.O. / Guan-Sheng, J. / Than, M.E.
CitationJournal: ACS Chem. Biol. / Year: 2017
Title: Structural Studies Revealed Active Site Distortions of Human Furin by a Small Molecule Inhibitor.
Authors: Dahms, S.O. / Jiao, G.S. / Than, M.E.
Validation Report
SummaryFull reportAbout validation report
History
DepositionNov 28, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 10, 2017Provider: repository / Type: Initial release
Revision 1.1May 31, 2017Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Furin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,81211
Polymers52,3891
Non-polymers1,42310
Water8,737485
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area730 Å2
ΔGint-60 kcal/mol
Surface area18200 Å2
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)132.204, 132.204, 155.727
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-606-

NA

21A-607-

NA

31A-1122-

HOH

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Components

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Protein/peptide , 1 types, 1 molecules A

#1: Protein/peptide Furin / / Dibasic-processing enzyme / Paired basic amino acid residue-cleaving enzyme / PACE


Mass: 52388.602 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FURIN, FUR, PACE, PCSK3 / Cell line (production host): HEK293S / Production host: Homo sapiens (human) / References: UniProt: P09958, furin

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Non-polymers , 5 types, 495 molecules

#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca / Calcium
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na / Sodium
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl / Chloride
#5: Chemical ChemComp-1N / 1-[(1~{R},2~{R},4~{S},5~{S})-2,4-bis(4-carbamimidamidophenoxy)-5-[(4-carbamimidamidophenyl)amino]cyclohexyl]guanidine


Mass: 587.679 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C28H37N13O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 485 / Source method: isolated from a natural source / Formula: H2O / Water

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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: 3.75 Å3/Da / Density % sol: 67.2 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: CRYSTALLIZATION SOLUTION: 100 MM MES, 200 MM K/NAH2PO4, PH 5.5-6.0, 3-4 M NACL, 3% DMSO; RESERVOIR SOLUTION: 3-4 M NACL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.918409 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 24, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918409 Å / Relative weight: 1
ReflectionResolution: 1.9→46.12 Å / Num. obs: 63025 / % possible obs: 99.2 % / Redundancy: 4.9 % / Biso Wilson estimate: 25.5 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.131 / Net I/σ(I): 11.04
Reflection shellResolution: 1.9→2.02 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.791 / Mean I/σ(I) obs: 2.17 / CC1/2: 0.732 / % possible all: 97.6

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5JXG
Resolution: 1.9→41.694 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 17.58
RfactorNum. reflection% reflection
Rfree0.1838 3071 4.87 %
Rwork0.1647 --
Obs0.1656 63009 99.16 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.9→41.694 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3608 0 94 485 4187
Refine LS restraints

Refinement-ID: X-RAY DIFFRACTION

TypeDev idealNumber
f_bond_d0.0073886
f_angle_d1.075312
f_dihedral_angle_d14.8961438
f_chiral_restr0.044573
f_plane_restr0.005709
LS refinement shell

Refinement-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.9003-1.930.29241400.2534260597
1.93-1.96170.27111390.2372265199
1.9617-1.99550.251130.2261266998
1.9955-2.03180.22331290.2195265998
2.0318-2.07090.23561410.205268299
2.0709-2.11310.21011560.19482670100
2.1131-2.15910.21371340.1832716100
2.1591-2.20930.23121400.1774268699
2.2093-2.26460.2081360.16852695100
2.2646-2.32580.22651250.17272729100
2.3258-2.39420.19091270.16422727100
2.3942-2.47150.20121300.17572717100
2.4715-2.55980.19211360.1695270899
2.5598-2.66230.2141230.1761272799
2.6623-2.78340.18661530.16962704100
2.7834-2.93010.21531480.1792743100
2.9301-3.11370.16861400.16512755100
3.1137-3.3540.17331520.15282750100
3.354-3.69130.15791510.13792769100
3.6913-4.2250.13941470.11872789100
4.225-5.32130.12441510.1249282999
5.3213-41.70410.16661600.1737295898

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