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- PDB-6qsx: Complement factor B protease domain in complex with the reversibl... -

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Basic information

Entry
Database: PDB / ID: 6qsx
TitleComplement factor B protease domain in complex with the reversible inhibitor ((2S,4S)-1-((5,7-dimethyl-1H-indol-4-yl)methyl)-4-methoxypiperidin-2-yl)methanol.
ComponentsComplement factor B
KeywordsHYDROLASE / Complement / immune / inhibitor / c3 convertase
Function / homology
Function and homology information


alternative-complement-pathway C3/C5 convertase / complement binding / Alternative complement activation / Activation of C3 and C5 / complement activation / complement activation, alternative pathway / Regulation of Complement cascade / response to bacterium / blood microparticle / serine-type endopeptidase activity ...alternative-complement-pathway C3/C5 convertase / complement binding / Alternative complement activation / Activation of C3 and C5 / complement activation / complement activation, alternative pathway / Regulation of Complement cascade / response to bacterium / blood microparticle / serine-type endopeptidase activity / proteolysis / extracellular space / extracellular exosome / extracellular region / plasma membrane
Similarity search - Function
Complement factor B / Complement B/C2 / Sushi repeat (SCR repeat) / Domain abundant in complement control proteins; SUSHI repeat; short complement-like repeat (SCR) / von Willebrand factor type A domain / Sushi/SCR/CCP domain / Sushi/CCP/SCR domain profile. / Sushi/SCR/CCP superfamily / VWFA domain profile. / von Willebrand factor (vWF) type A domain ...Complement factor B / Complement B/C2 / Sushi repeat (SCR repeat) / Domain abundant in complement control proteins; SUSHI repeat; short complement-like repeat (SCR) / von Willebrand factor type A domain / Sushi/SCR/CCP domain / Sushi/CCP/SCR domain profile. / Sushi/SCR/CCP superfamily / VWFA domain profile. / von Willebrand factor (vWF) type A domain / von Willebrand factor, type A / von Willebrand factor A-like domain superfamily / 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 / Peptidase S1, PA clan
Similarity search - Domain/homology
Chem-JGN / Complement factor B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.77 Å
AuthorsAdams, C.M. / Sellner, H. / Ehara, T. / Mac Sweeney, A. / Crowley, M. / Anderson, K. / Karki, R. / Mainolfi, N. / Valeur, E. / Sirockin, F. ...Adams, C.M. / Sellner, H. / Ehara, T. / Mac Sweeney, A. / Crowley, M. / Anderson, K. / Karki, R. / Mainolfi, N. / Valeur, E. / Sirockin, F. / Gerhartz, B. / Erbel, P. / Hughes, N. / Smith, T.M. / Cumin, F. / Argikar, U. / Mogi, M. / Sedrani, R. / Wiesmann, C. / Jaffee, B. / Maibaum, J. / Flohr, S. / Harrison, R. / Eder, J.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2019
Title: Small-molecule factor B inhibitor for the treatment of complement-mediated diseases.
Authors: Schubart, A. / Anderson, K. / Mainolfi, N. / Sellner, H. / Ehara, T. / Adams, C.M. / Mac Sweeney, A. / Liao, S.M. / Crowley, M. / Littlewood-Evans, A. / Sarret, S. / Wieczorek, G. / Perrot, ...Authors: Schubart, A. / Anderson, K. / Mainolfi, N. / Sellner, H. / Ehara, T. / Adams, C.M. / Mac Sweeney, A. / Liao, S.M. / Crowley, M. / Littlewood-Evans, A. / Sarret, S. / Wieczorek, G. / Perrot, L. / Dubost, V. / Flandre, T. / Zhang, Y. / Smith, R.J.H. / Risitano, A.M. / Karki, R.G. / Zhang, C. / Valeur, E. / Sirockin, F. / Gerhartz, B. / Erbel, P. / Hughes, N. / Smith, T.M. / Cumin, F. / Argikar, U.A. / Haraldsson, B. / Mogi, M. / Sedrani, R. / Wiesmann, C. / Jaffee, B. / Maibaum, J. / Flohr, S. / Harrison, R. / Eder, J.
History
DepositionFeb 22, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 27, 2019Provider: repository / Type: Initial release
Revision 1.1Aug 14, 2019Group: Data collection / Structure summary / Category: pdbx_poly_seq_scheme / Item: _pdbx_poly_seq_scheme.auth_seq_num
Revision 1.2Sep 18, 2019Group: Data collection / Structure summary / Category: pdbx_poly_seq_scheme / Item: _pdbx_poly_seq_scheme.auth_seq_num
Revision 1.3Oct 9, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.4Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry
Revision 1.5Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AAA: Complement factor B
BBB: Complement factor B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,32013
Polymers65,9122
Non-polymers1,40811
Water6,900383
1
AAA: Complement factor B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,5465
Polymers32,9561
Non-polymers5914
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
BBB: Complement factor B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,7738
Polymers32,9561
Non-polymers8177
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.592, 98.060, 61.721
Angle α, β, γ (deg.)90.000, 99.174, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain: (Details: Chains A B)

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Components

#1: Protein Complement factor B / C3/C5 convertase / Glycine-rich beta glycoprotein / GBG / PBF2 / Properdin factor B


Mass: 32955.883 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CFB, BF, BFD / Production host: Drosophila sp. (fry)
References: UniProt: P00751, alternative-complement-pathway C3/C5 convertase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-JGN / [(2~{S},4~{S})-1-[(5,7-dimethyl-1~{H}-indol-4-yl)methyl]-4-methoxy-piperidin-2-yl]methanol


Mass: 302.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H26N2O2
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 383 / 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: 2.52 Å3/Da / Density % sol: 51.19 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 2.5 M ammonium sulfate, 0.1 mM sodium acetate (pH 4.6), 2 mM inhibitor

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jun 1, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.77→51.754 Å / Num. obs: 63253 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 3.4 % / Rrim(I) all: 0.052 / Net I/σ(I): 16.56
Reflection shellResolution: 1.77→1.83 Å / Redundancy: 3.5 % / Mean I/σ(I) obs: 4.25 / Num. unique obs: 6010 / Rrim(I) all: 0.33 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0238 2018/15/10refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1DLE

1dle


Resolution: 1.77→51.754 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.943 / SU B: 2.802 / SU ML: 0.086 / Cross valid method: FREE R-VALUE / ESU R: 0.12 / ESU R Free: 0.114
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2198 3163 -
Rwork0.1894 --
all0.191 --
obs-63252 99.511 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 24.277 Å2
Baniso -1Baniso -2Baniso -3
1--0.051 Å2-0 Å2-0.085 Å2
2--0.095 Å20 Å2
3----0.016 Å2
Refinement stepCycle: LAST / Resolution: 1.77→51.754 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4463 0 81 383 4927
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0134663
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174248
X-RAY DIFFRACTIONr_angle_refined_deg1.5991.6616334
X-RAY DIFFRACTIONr_angle_other_deg1.361.5819899
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.795573
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.04123.08224
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.55515795
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.4561523
X-RAY DIFFRACTIONr_chiral_restr0.0820.2595
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.025133
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02908
X-RAY DIFFRACTIONr_nbd_refined0.1920.2820
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1820.24095
X-RAY DIFFRACTIONr_nbtor_refined0.1650.22210
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0790.22102
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1290.2308
X-RAY DIFFRACTIONr_metal_ion_refined0.0330.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.190.219
X-RAY DIFFRACTIONr_nbd_other0.1860.235
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1020.217
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.0480.22
X-RAY DIFFRACTIONr_mcbond_it2.0152.3482289
X-RAY DIFFRACTIONr_mcbond_other2.0122.3482288
X-RAY DIFFRACTIONr_mcangle_it2.7883.5132857
X-RAY DIFFRACTIONr_mcangle_other2.7893.5142858
X-RAY DIFFRACTIONr_scbond_it3.22.7412374
X-RAY DIFFRACTIONr_scbond_other3.1432.7322298
X-RAY DIFFRACTIONr_scangle_it4.8263.9453475
X-RAY DIFFRACTIONr_scangle_other4.783.9273365
X-RAY DIFFRACTIONr_lrange_it5.79928.2055118
X-RAY DIFFRACTIONr_lrange_other5.77528.14953
X-RAY DIFFRACTIONr_ncsr_local_group_10.0930.058859
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)WRfactor Rwork
1.77-1.8160.2842350.2544469470599.97870.201
1.816-1.8660.2652260.2274298452599.97790.178
1.866-1.920.3242210.2894198444999.32570.223
1.92-1.9790.2442150.2234079430599.74450.178
1.979-2.0430.2542090.1993965417899.90430.169
2.043-2.1150.2132010.1933833404999.62950.167
2.115-2.1950.2541940.1973685389899.51260.174
2.195-2.2840.2621840.2333484374697.91780.188
2.284-2.3860.2071810.1833438362799.77940.168
2.386-2.5020.1981710.1713258343599.82530.159
2.502-2.6370.2091640.1663116328799.7870.159
2.637-2.7960.2331550.1792945311699.48650.176
2.796-2.9890.2431440.192739290699.20850.191
2.989-3.2270.2121360.1852578273399.30480.192
3.227-3.5340.2391240.1892359249699.47920.199
3.534-3.9490.2011140.1762157228499.43080.19
3.949-4.5550.139990.1491897201099.30350.172
4.555-5.5680.207860.1611624172099.41860.189
5.568-7.8290.198660.1831248132799.02030.213
7.829-51.7540.207380.20371976598.95420.238

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