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- PDB-6ftz: COMPLEMENT FACTOR D COMPLEXED WITH COMPOUND 6 -

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Basic information

Entry
Database: PDB / ID: 6ftz
TitleCOMPLEMENT FACTOR D COMPLEXED WITH COMPOUND 6
ComponentsComplement factor D
KeywordsHYDROLASE / SERINE PROTEASE
Function / homology
Function and homology information


complement factor D / Alternative complement activation / complement activation / complement activation, alternative pathway / serine-type peptidase activity / platelet alpha granule lumen / protein maturation / response to bacterium / Platelet degranulation / secretory granule lumen ...complement factor D / Alternative complement activation / complement activation / complement activation, alternative pathway / serine-type peptidase activity / platelet alpha granule lumen / protein maturation / response to bacterium / Platelet degranulation / secretory granule lumen / ficolin-1-rich granule lumen / serine-type endopeptidase activity / Neutrophil degranulation / proteolysis / extracellular space / extracellular exosome / extracellular region
Similarity search - Function
Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Serine proteases, trypsin family, histidine active site. / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, serine active site. / Serine proteases, trypsin domain profile. / 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 / Serine proteases, trypsin family, histidine active site. / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, serine active site. / Serine proteases, trypsin domain profile. / 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-E7E / Complement factor D
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.67 Å
AuthorsOstermann, N.
CitationJournal: ACS Med Chem Lett / Year: 2018
Title: Discovery and Design of First Benzylamine-Based Ligands Binding to an Unlocked Conformation of the Complement Factor D.
Authors: Vulpetti, A. / Ostermann, N. / Randl, S. / Yoon, T. / Mac Sweeney, A. / Cumin, F. / Lorthiois, E. / Rudisser, S. / Erbel, P. / Maibaum, J.
History
DepositionFeb 26, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 6, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Complement factor D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,0472
Polymers24,7391
Non-polymers3081
Water3,765209
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area10100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.220, 49.975, 39.370
Angle α, β, γ (deg.)90.00, 106.07, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 24739.121 Da / Num. of mol.: 1
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-E7E / ~{N}4-[3-(aminomethyl)phenyl]-1~{H}-indole-2,4-dicarboxamide


Mass: 308.335 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H16N4O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 209 / Source method: isolated from a natural source / Formula: H2O
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: 2.11 Å3/Da / Density % sol: 41.71 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / Details: PEG3350, 100 mM HEPES pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 12, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.67→49.98 Å / Num. obs: 23397 / % possible obs: 97.1 % / Redundancy: 3.09 % / Biso Wilson estimate: 11.64 Å2 / Rmerge(I) obs: 0.055 / Net I/σ(I): 10.62
Reflection shellResolution: 1.67→1.74 Å / Redundancy: 2.91 % / Rmerge(I) obs: 0.197 / Mean I/σ(I) obs: 5.53 / % possible all: 90.6

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
BUSTER2.11.7refinement
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5FBE

5fbe


Resolution: 1.67→18.7 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.9 / SU R Cruickshank DPI: 0.105 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.111 / SU Rfree Blow DPI: 0.111 / SU Rfree Cruickshank DPI: 0.108
RfactorNum. reflection% reflectionSelection details
Rfree0.22 1169 5 %RANDOM
Rwork0.173 ---
obs0.175 23386 97.3 %-
Displacement parametersBiso mean: 16.11 Å2
Baniso -1Baniso -2Baniso -3
1-3.0006 Å20 Å2-1.9285 Å2
2---2.714 Å20 Å2
3----0.2865 Å2
Refine analyzeLuzzati coordinate error obs: 0.21 Å
Refinement stepCycle: LAST / Resolution: 1.67→18.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1712 0 23 209 1944
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.011847HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.092531HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d634SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes40HARMONIC2
X-RAY DIFFRACTIONt_gen_planes285HARMONIC5
X-RAY DIFFRACTIONt_it1847HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.54
X-RAY DIFFRACTIONt_other_torsion15.74
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion228SEMIHARMONIC5
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_contact2279SEMIHARMONIC4
LS refinement shellResolution: 1.67→1.74 Å / Total num. of bins used: 12
RfactorNum. reflection% reflection
Rfree0.2761 131 4.98 %
Rwork0.2334 2497 -
all0.2356 2628 -
obs--91.16 %

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