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- PDB-5nb7: Complement factor D -

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Basic information

Entry
Database: PDB / ID: 5nb7
TitleComplement factor D
ComponentsComplement factor D
KeywordsHYDROLASE
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-8NQ / Complement factor D
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.33 Å
AuthorsMac Sweeney, A. / Ostermann, N.
CitationJournal: J. Med. Chem. / Year: 2017
Title: Discovery of Highly Potent and Selective Small-Molecule Reversible Factor D Inhibitors Demonstrating Alternative Complement Pathway Inhibition in Vivo.
Authors: Lorthiois, E. / Anderson, K. / Vulpetti, A. / Rogel, O. / Cumin, F. / Ostermann, N. / Steinbacher, S. / Mac Sweeney, A. / Delgado, O. / Liao, S.M. / Randl, S. / Rudisser, S. / Dussauge, S. / ...Authors: Lorthiois, E. / Anderson, K. / Vulpetti, A. / Rogel, O. / Cumin, F. / Ostermann, N. / Steinbacher, S. / Mac Sweeney, A. / Delgado, O. / Liao, S.M. / Randl, S. / Rudisser, S. / Dussauge, S. / Fettis, K. / Kieffer, L. / de Erkenez, A. / Yang, L. / Hartwieg, C. / Argikar, U.A. / La Bonte, L.R. / Newton, R. / Kansara, V. / Flohr, S. / Hommel, U. / Jaffee, B. / Maibaum, J.
History
DepositionMar 1, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 28, 2017Provider: repository / Type: Initial release
Revision 1.1Jul 26, 2017Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_id_ASTM ..._citation.country / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.name
Revision 1.2Jan 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 1.3Nov 6, 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)25,2374
Polymers24,5971
Non-polymers6403
Water3,873215
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area420 Å2
ΔGint3 kcal/mol
Surface area9860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.801, 49.884, 39.088
Angle α, β, γ (deg.)90.00, 106.08, 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: 24596.965 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-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#3: Chemical ChemComp-8NQ / 1-[2-[(1~{R},3~{S},5~{R})-3-[(6-bromanylpyridin-2-yl)carbamoyl]-2-azabicyclo[3.1.0]hexan-2-yl]-2-oxidanylidene-ethyl]indazole-3-carboxamide


Mass: 483.318 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H19BrN6O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 215 / 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: 2.13 Å3/Da / Density % sol: 42.12 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: 22% PEG 3350, 0.1 m HEPES pH 7.5, 50 mM NaCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: May 5, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.33→30 Å / Num. obs: 47029 / % possible obs: 99 % / Redundancy: 3.3 % / Net I/σ(I): 18.51
Reflection shellResolution: 1.33→1.39 Å / Mean I/σ(I) obs: 3.6 / Num. unique obs: 5778 / % possible all: 98.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1DSU

1dsu


Resolution: 1.33→29.07 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.96 / SU B: 2.141 / SU ML: 0.04 / Cross valid method: THROUGHOUT / ESU R: 0.051 / ESU R Free: 0.056 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19582 2351 5 %RANDOM
Rwork0.14025 ---
obs0.14299 44675 99.07 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.658 Å2
Baniso -1Baniso -2Baniso -3
1--0.47 Å20 Å20.12 Å2
2---0.64 Å20 Å2
3---0.9 Å2
Refinement stepCycle: 1 / Resolution: 1.33→29.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1701 0 39 215 1955
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.030.0191789
X-RAY DIFFRACTIONr_bond_other_d0.0010.021647
X-RAY DIFFRACTIONr_angle_refined_deg2.561.9592446
X-RAY DIFFRACTIONr_angle_other_deg2.0062.9863812
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6335233
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.52623.23971
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.7115270
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.011514
X-RAY DIFFRACTIONr_chiral_restr0.5220.2278
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.0212025
X-RAY DIFFRACTIONr_gen_planes_other0.0120.02343
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_it3.0061.554923
X-RAY DIFFRACTIONr_mcbond_other2.9871.551922
X-RAY DIFFRACTIONr_mcangle_it3.4132.3451153
X-RAY DIFFRACTIONr_mcangle_other3.4162.3481154
X-RAY DIFFRACTIONr_scbond_it4.5751.954866
X-RAY DIFFRACTIONr_scbond_other4.5641.955865
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.0512.7771289
X-RAY DIFFRACTIONr_long_range_B_refined4.94820.7631980
X-RAY DIFFRACTIONr_long_range_B_other4.94720.7561981
X-RAY DIFFRACTIONr_rigid_bond_restr6.35233436
X-RAY DIFFRACTIONr_sphericity_free31.4675145
X-RAY DIFFRACTIONr_sphericity_bonded13.58653463
LS refinement shellResolution: 1.33→1.364 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.258 171 -
Rwork0.214 3250 -
obs--98.45 %

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