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

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Basic information

Entry
Database: PDB / ID: 6qsw
TitleComplement factor B protease domain in complex with the reversible inhibitor N-(2-bromo-4-methylnaphthalen-1-yl)-4,5-dihydro-1H-imidazol-2-amine.
ComponentsComplement factor B
KeywordsHYDROLASE / Complement / immune / inhibitor / c3 convertase
Function / homology
Function and homology information


alternative-complement-pathway C3/C5 convertase / classical-complement-pathway C3/C5 convertase complex / complement binding / Alternative complement activation / Activation of C3 and C5 / complement activation, alternative pathway / complement activation / Regulation of Complement cascade / response to bacterium / blood microparticle ...alternative-complement-pathway C3/C5 convertase / classical-complement-pathway C3/C5 convertase complex / complement binding / Alternative complement activation / Activation of C3 and C5 / complement activation, alternative pathway / complement activation / 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) / Sushi/SCR/CCP domain / Sushi/SCR/CCP superfamily / von Willebrand factor type A domain / Sushi/CCP/SCR domain profile. / von Willebrand factor (vWF) type A domain / VWFA domain profile. ...Complement factor B / Complement B/C2 / Sushi repeat (SCR repeat) / Domain abundant in complement control proteins; SUSHI repeat; short complement-like repeat (SCR) / Sushi/SCR/CCP domain / Sushi/SCR/CCP superfamily / von Willebrand factor type A domain / Sushi/CCP/SCR domain profile. / von Willebrand factor (vWF) type A domain / VWFA domain profile. / 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 / 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 / Peptidase S1, PA clan
Similarity search - Domain/homology
Chem-JGT / Complement factor B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.64 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 / Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name
Revision 1.2Sep 18, 2019Group: Data collection / Structure summary / Category: pdbx_poly_seq_scheme / Item: _pdbx_poly_seq_scheme.auth_seq_num
Revision 1.3Nov 20, 2019Group: Structure summary / Category: pdbx_poly_seq_scheme / Item: _pdbx_poly_seq_scheme.auth_seq_num
Revision 1.4Apr 8, 2020Group: 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 1.5Jan 24, 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

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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
CCC: Complement factor B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,74116
Polymers98,8683
Non-polymers1,87313
Water9,008500
1
AAA: Complement factor B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,5485
Polymers32,9561
Non-polymers5924
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
BBB: Complement factor B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,6446
Polymers32,9561
Non-polymers6885
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
CCC: Complement factor B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,5485
Polymers32,9561
Non-polymers5924
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)91.281, 91.281, 260.221
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11CCC-491-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11Chains A B
22Chains A C
33Chains B C

NCS ensembles :
ID
1
2
3

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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.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CFB, BF, BFD / Production host: Drosophila melanogaster (fruit fly)
References: UniProt: P00751, alternative-complement-pathway C3/C5 convertase
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-JGT / ~{N}-(2-bromanyl-4-methyl-naphthalen-1-yl)-4,5-dihydro-1~{H}-imidazol-2-amine


Mass: 304.185 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C14H14BrN3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 500 / 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: 2.74 Å3/Da / Density % sol: 55.13 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 2.0 M ammonium sulfate, 0.1 M 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: 1.001 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jun 1, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.001 Å / Relative weight: 1
ReflectionResolution: 1.64→65.1 Å / Num. obs: 129551 / % possible obs: 95.8 % / Redundancy: 7.6 % / Rrim(I) all: 0.068 / Net I/σ(I): 19.56
Reflection shellResolution: 1.64→1.7 Å / Redundancy: 2.64 % / Mean I/σ(I) obs: 2.52 / Num. unique obs: 10441 / Rrim(I) all: 0.44 / % possible all: 76.6

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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: 1.64→65.055 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.952 / SU B: 3.677 / SU ML: 0.054 / Cross valid method: FREE R-VALUE / ESU R: 0.089 / ESU R Free: 0.075
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1881 6478 -
Rwork0.1567 --
all0.158 --
obs-129548 95.837 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 21.87 Å2
Baniso -1Baniso -2Baniso -3
1-1.028 Å2-0 Å2-0 Å2
2--1.028 Å2-0 Å2
3----2.056 Å2
Refinement stepCycle: LAST / Resolution: 1.64→65.055 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6222 0 104 500 6826
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0136536
X-RAY DIFFRACTIONr_bond_other_d0.0020.0176035
X-RAY DIFFRACTIONr_angle_refined_deg1.4051.6568876
X-RAY DIFFRACTIONr_angle_other_deg1.3141.58114044
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5685799
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.91122.797311
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.239151114
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.331533
X-RAY DIFFRACTIONr_chiral_restr0.0690.2830
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.027161
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021288
X-RAY DIFFRACTIONr_nbd_refined0.1990.21081
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1870.25600
X-RAY DIFFRACTIONr_nbtor_refined0.1640.23075
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0770.22808
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1080.2387
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1430.223
X-RAY DIFFRACTIONr_nbd_other0.1950.268
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1640.229
X-RAY DIFFRACTIONr_mcbond_it2.472.0143193
X-RAY DIFFRACTIONr_mcbond_other2.472.0143192
X-RAY DIFFRACTIONr_mcangle_it3.0543.0163972
X-RAY DIFFRACTIONr_mcangle_other3.0543.0163973
X-RAY DIFFRACTIONr_scbond_it2.9052.4663343
X-RAY DIFFRACTIONr_scbond_other2.8492.4623243
X-RAY DIFFRACTIONr_scangle_it3.5573.5294897
X-RAY DIFFRACTIONr_scangle_other3.4933.5144753
X-RAY DIFFRACTIONr_lrange_it4.07824.1067099
X-RAY DIFFRACTIONr_lrange_other4.03424.0996874
X-RAY DIFFRACTIONr_rigid_bond_restr1.72312565
X-RAY DIFFRACTIONr_ncsr_local_group_10.080.057996
X-RAY DIFFRACTIONr_ncsr_local_group_20.0730.058075
X-RAY DIFFRACTIONr_ncsr_local_group_30.0880.058055
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
1.64-1.6830.2473710.2387048985175.31210.218
1.683-1.7290.2483970.2017549960682.71910.178
1.729-1.7790.2144180.1717928935389.23340.148
1.779-1.8330.2144320.1548223908795.2460.131
1.833-1.8940.1944390.1398329880799.55720.119
1.894-1.960.1774270.1288115855599.8480.112
1.96-2.0340.2014130.1317843826099.95160.118
2.034-2.1170.1733970.126754379401000.115
2.117-2.2110.1753820.126725576371000.117
2.211-2.3190.1693650.126694973141000.12
2.319-2.4440.1693490.1316626697699.98570.127
2.444-2.5920.1913310.146629066211000.144
2.592-2.770.1763110.146591662271000.149
2.77-2.9920.1752910.1555526581899.98280.162
2.992-3.2770.1852700.175127539899.98150.183
3.277-3.6630.192450.1654648489499.97960.185
3.663-4.2270.1752170.1574131435099.9540.185
4.227-5.1710.191870.1643553374299.94660.195
5.171-7.290.2171480.2172811296099.96620.257
7.29-65.0550.196880.2291661177898.3690.323

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