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- PDB-5fbe: COMPLEMENT FACTOR D IN COMPLEX WITH COMPOUND2 -

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Basic information

Entry
Database: PDB / ID: 5fbe
TitleCOMPLEMENT FACTOR D IN COMPLEX WITH COMPOUND2
ComponentsComplement factor DFactor D
KeywordsHYDROLASE
Function / homology
Function and homology information


complement factor D / Alternative complement activation / complement activation, alternative pathway / complement activation / serine-type peptidase activity / platelet alpha granule lumen / response to bacterium / Platelet degranulation / secretory granule lumen / ficolin-1-rich granule lumen ...complement factor D / Alternative complement activation / complement activation, alternative pathway / complement activation / serine-type peptidase activity / platelet alpha granule lumen / response to bacterium / Platelet degranulation / secretory granule lumen / ficolin-1-rich granule lumen / serine-type endopeptidase activity / Neutrophil degranulation / proteolysis / extracellular exosome / extracellular region
Similarity search - Function
Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, histidine active site. / Serine proteases, trypsin domain profile. / Serine proteases, trypsin family, serine active site. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Trypsin-like serine proteases ...Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, histidine active site. / Serine proteases, trypsin domain profile. / Serine proteases, trypsin family, serine active site. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Trypsin-like serine proteases / Thrombin, subunit H / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Chem-5W5 / Complement factor D
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.43 Å
AuthorsOstermann, N. / Zink, F.
CitationJournal: Nat.Chem.Biol. / Year: 2016
Title: Small-molecule factor D inhibitors targeting the alternative complement pathway.
Authors: Maibaum, J. / Liao, S.M. / Vulpetti, A. / Ostermann, N. / Randl, S. / Rudisser, S. / Lorthiois, E. / Erbel, P. / Kinzel, B. / Kolb, F.A. / Barbieri, S. / Wagner, J. / Durand, C. / Fettis, K. ...Authors: Maibaum, J. / Liao, S.M. / Vulpetti, A. / Ostermann, N. / Randl, S. / Rudisser, S. / Lorthiois, E. / Erbel, P. / Kinzel, B. / Kolb, F.A. / Barbieri, S. / Wagner, J. / Durand, C. / Fettis, K. / Dussauge, S. / Hughes, N. / Delgado, O. / Hommel, U. / Gould, T. / Mac Sweeney, A. / Gerhartz, B. / Cumin, F. / Flohr, S. / Schubart, A. / Jaffee, B. / Harrison, R. / Risitano, A.M. / Eder, J. / Anderson, K.
History
DepositionDec 14, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Oct 26, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 2, 2016Group: Database references
Revision 1.2Nov 23, 2016Group: Database references
Revision 1.3Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Complement factor D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,2973
Polymers24,7391
Non-polymers5582
Water3,675204
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area250 Å2
ΔGint-0 kcal/mol
Surface area9940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.400, 50.000, 39.358
Angle α, β, γ (deg.)90.00, 105.75, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Complement factor D / Factor D / Adipsin / C3 convertase activator / Properdin factor D


Mass: 24739.121 Da / Num. of mol.: 1 / Fragment: UNP residues 26-253
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CFD, DF, PFD / Production host: Escherichia coli (E. coli) / References: UniProt: P00746, complement factor D
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-5W5 / methyl 2-[[[(2~{S})-2-[[3-(trifluoromethyloxy)phenyl]carbamoyl]pyrrolidin-1-yl]carbonylamino]methyl]benzoate


Mass: 465.422 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H22F3N3O5
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 204 / 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: 2.12 Å3/Da / Density % sol: 42 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 1 MICROLITER PROTEIN SOLUTION WAS MIXED WITH 1 MICROLITER RESERVOIR SOLUTION. PROTEIN SOLUTION: 18 mg/mL FD, 10 mM Tris pH 7.0, 100 mM NaCl; RESERVOIR SOLUTION: 22% PEG3350, 100 mM HEPES pH ...Details: 1 MICROLITER PROTEIN SOLUTION WAS MIXED WITH 1 MICROLITER RESERVOIR SOLUTION. PROTEIN SOLUTION: 18 mg/mL FD, 10 mM Tris pH 7.0, 100 mM NaCl; RESERVOIR SOLUTION: 22% PEG3350, 100 mM HEPES pH 7.5; SOAKING AND CRYO: ADDITION of 10 mM COMPOUND2 for 45 min FOLLOWED by the ADDITION OF 0.5 MICROLITER GLYCEROL AND FLASH FREEZING IN LIQUIT NITROGEN.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9999 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 10, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9999 Å / Relative weight: 1
ReflectionResolution: 1.43→16.1 Å / Num. obs: 38106 / % possible obs: 99.2 % / Redundancy: 3.7 % / Biso Wilson estimate: 18.18 Å2 / Rmerge(I) obs: 0.055 / Net I/σ(I): 12.4
Reflection shellResolution: 1.43→1.47 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 3.6 / % possible all: 95

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
BUSTER2.11.5refinement
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1BIO

1bio


Resolution: 1.43→16.1 Å / Cor.coef. Fo:Fc: 0.9631 / Cor.coef. Fo:Fc free: 0.9584 / SU R Cruickshank DPI: 0.063 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.064 / SU Rfree Blow DPI: 0.063 / SU Rfree Cruickshank DPI: 0.062
RfactorNum. reflection% reflectionSelection details
Rfree0.1879 1904 5 %RANDOM
Rwork0.1687 ---
obs0.1697 38094 99.35 %-
Displacement parametersBiso mean: 22.17 Å2
Baniso -1Baniso -2Baniso -3
1--0.4395 Å20 Å2-0.3468 Å2
2--0.1133 Å20 Å2
3---0.3262 Å2
Refine analyzeLuzzati coordinate error obs: 0.143 Å
Refinement stepCycle: LAST / Resolution: 1.43→16.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1783 0 39 204 2026
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.011871HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.112563HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d647SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes40HARMONIC2
X-RAY DIFFRACTIONt_gen_planes288HARMONIC5
X-RAY DIFFRACTIONt_it1871HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.95
X-RAY DIFFRACTIONt_other_torsion14.46
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion230SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact2366SEMIHARMONIC4
LS refinement shellResolution: 1.43→1.47 Å / Total num. of bins used: 19
RfactorNum. reflection% reflection
Rfree0.2354 148 4.98 %
Rwork0.1956 2824 -
all0.1978 2972 -
obs--99.35 %

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