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1rtk

Crystal Structure Analysis of the Bb segment of Factor B complexed with 4-guanidinobenzoic acid

Method: X-RAY DIFFRACTION Dmax: 89.5 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Complement factor B Bb fragment

Homo sapiens

UniProt P00751

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain A； UniProt 268–764 Fragment：COMPLEMENT FACTOR B BB FRAGMENT Mutation：F428C, N435C, C267V IOD IODIDE ION × 2 NA SODIUM ION × 7 MG MAGNESIUM ION × 1 GBS 4-carbamimidamidobenzoic acid × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；298 K；PEGMME 2000, NaI, VAPOR DIFFUSION, HANGING DROP, temperature 298K Resolution 2.30 Å R-free 0.245

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 1RTK Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1DLE FACTOR B SERINE PROTEASE DOMAIN Deposited 1999-12-09 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 470–764（295 aa） Fragment：SERINE PROTEASE DOMAIN
Chain B 470–764（295 aa） Fragment：SERINE PROTEASE DOMAIN
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；PEG-1000, MES, TRIS, SODIUM CHLORIDE, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.10 Å R-free 0.249
1Q0P A domain of Factor B Deposited 2003-07-17 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 254–476（223 aa） Fragment：sequence database residues 254-476
Mutation：C267S MN MANGANESE (II) ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；277 K；30% Jeffamine, 0.05M Ceseium Chloride, 0.1M MES, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Resolution 1.80 Å R-free 0.259
1RRK Crystal Structure Analysis of the Bb segment of Factor B Deposited 2003-12-08 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 243–764（522 aa） Fragment：COMPLEMENT FACTOR B BB FRAGMENT
Mutation：F428C, N435C, C267V IOD IODIDE ION × 2 NA SODIUM ION × 7 CO COBALT (II) ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；PEGMME 2000, NaI, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Resolution 2.00 Å R-free 0.245
1RS0 Crystal Structure Analysis of the Bb segment of Factor B complexed with Di-isopropyl-phosphate (DIP) Deposited 2003-12-09 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 268–764（497 aa） Fragment：COMPLEMENT FACTOR B BB FRAGMENT
Mutation：F428C, N435C, C267V IOD IODIDE ION × 2 NA SODIUM ION × 7 MG MAGNESIUM ION × 1 DFP DIISOPROPYL PHOSPHONATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；PEGMME 2000, NaI, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Resolution 2.60 Å R-free 0.251
2OK5 Human Complement factor B Deposited 2007-01-16 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric
Chain A 26–764（739 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 GOL GLYCEROL × 13 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；12% PEG 1500, 0.02 M Malic acid, 0.04 M MES, 0.04 M TRIS, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.30 Å R-free 0.241
2WIN C3 convertase (C3bBb) stabilized by SCIN Deposited 2009-05-13 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 8 PDB declaration: octameric
Chain J 260–764（505 aa） Fragment：COMPLEMENT FACTOR B BB FRAGMENT, RESIDUES 260-764
Chain L 260–764（505 aa） Fragment：COMPLEMENT FACTOR B BB FRAGMENT, RESIDUES 260-764
Not recorded MAN alpha-D-mannopyranose × 1 BMA beta-D-mannopyranose × 1 MG MAGNESIUM ION × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.5；75 MM SODIUM/POTASSIUM TARTRATE, 8.0% PEG 3350, 50 MM BIS-TRIS PROPANE, PH 6.5
Resolution 3.90 Å R-free 0.268
2WIN C3 convertase (C3bBb) stabilized by SCIN Deposited 2009-05-13 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Other combination Heteromer；Protein × 8 PDB declaration: octameric
Chain I 260–764（505 aa） Fragment：COMPLEMENT FACTOR B BB FRAGMENT, RESIDUES 260-764
Chain K 260–764（505 aa） Fragment：COMPLEMENT FACTOR B BB FRAGMENT, RESIDUES 260-764
Not recorded BMA beta-D-mannopyranose × 1 MG MAGNESIUM ION × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.5；75 MM SODIUM/POTASSIUM TARTRATE, 8.0% PEG 3350, 50 MM BIS-TRIS PROPANE, PH 6.5
Resolution 3.90 Å R-free 0.268
2XWB Crystal Structure of Complement C3b in complex with Factors B and D Deposited 2010-11-01 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric
Chain F 35–764（730 aa） Fragment：RESIDUES 35-764
Mutation：YES MG MAGNESIUM ION × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.7；PH 7.7
Resolution 3.49 Å R-free 0.244
2XWB Crystal Structure of Complement C3b in complex with Factors B and D Deposited 2010-11-01 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric
Chain H 35–764（730 aa） Fragment：RESIDUES 35-764
Mutation：YES MG MAGNESIUM ION × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.7；PH 7.7
Resolution 3.49 Å R-free 0.244
2XWB Crystal Structure of Complement C3b in complex with Factors B and D Deposited 2010-11-01 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric
Chain H 35–764（730 aa） Fragment：RESIDUES 35-764
Mutation：YES MG MAGNESIUM ION × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.7；PH 7.7
Resolution 3.49 Å R-free 0.244
2XWB Crystal Structure of Complement C3b in complex with Factors B and D Deposited 2010-11-01 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric
Chain F 35–764（730 aa） Fragment：RESIDUES 35-764
Mutation：YES MG MAGNESIUM ION × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.7；PH 7.7
Resolution 3.49 Å R-free 0.244
2XWJ Crystal Structure of Complement C3b in Complex with Factor B Deposited 2010-11-04 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain I 26–764（739 aa） Fragment：COMPLEMENT FACTOR B
Mutation：YES NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 NI NICKEL (II) ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 4；pH 4.0
Resolution 4.00 Å R-free 0.281
2XWJ Crystal Structure of Complement C3b in Complex with Factor B Deposited 2010-11-04 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain J 26–764（739 aa） Fragment：COMPLEMENT FACTOR B
Mutation：YES NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 NI NICKEL (II) ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 4；pH 4.0
Resolution 4.00 Å R-free 0.281
2XWJ Crystal Structure of Complement C3b in Complex with Factor B Deposited 2010-11-04 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain L 26–764（739 aa） Fragment：COMPLEMENT FACTOR B
Mutation：YES NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 NI NICKEL (II) ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 4；pH 4.0
Resolution 4.00 Å R-free 0.281
2XWJ Crystal Structure of Complement C3b in Complex with Factor B Deposited 2010-11-04 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain K 26–764（739 aa） Fragment：COMPLEMENT FACTOR B
Mutation：YES NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 NI NICKEL (II) ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 4；pH 4.0
Resolution 4.00 Å R-free 0.281
3HRZ Cobra Venom Factor (CVF) in complex with human factor B Deposited 2009-06-10 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric
Chain D 26–764（739 aa） Fragment：residues 26-764
Mutation：D279G,N285D NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 MG MAGNESIUM ION × 2 K POTASSIUM ION × 1 P6G HEXAETHYLENE GLYCOL × 2 PO4 PHOSPHATE ION × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；291 K；PEG 3350, PEG 400, Na/K Phosphate, Bis-Tris propane, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Resolution 2.20 Å R-free 0.226
3HS0 Cobra Venom Factor (CVF) in complex with human factor B Deposited 2009-06-10 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric
Chain I 26–764（739 aa） Fragment：residues 26-764
Mutation：D279G,N285D NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 MG MAGNESIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 9；291 K；PEG 1500, 2,3 butanediol, malic acid 2-(N-morpholino)ethanesulfonic acid tris (hydroxymethyl)aminomethane buffer (MMT), pH 9.0, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Resolution 3.00 Å R-free 0.243
3HS0 Cobra Venom Factor (CVF) in complex with human factor B Deposited 2009-06-10 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric
Chain D 26–764（739 aa） Fragment：residues 26-764
Mutation：D279G,N285D NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 MG MAGNESIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 9；291 K；PEG 1500, 2,3 butanediol, malic acid 2-(N-morpholino)ethanesulfonic acid tris (hydroxymethyl)aminomethane buffer (MMT), pH 9.0, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Resolution 3.00 Å R-free 0.243
3HS0 Cobra Venom Factor (CVF) in complex with human factor B Deposited 2009-06-10 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Other combination Heteromer；Protein × 8 PDB declaration: octameric
Chain D 26–764（739 aa） Fragment：residues 26-764
Chain I 26–764（739 aa） Fragment：residues 26-764
Mutation：D279G,N285D Mutation：D279G,N285D NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 7 MG MAGNESIUM ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 9；291 K；PEG 1500, 2,3 butanediol, malic acid 2-(N-morpholino)ethanesulfonic acid tris (hydroxymethyl)aminomethane buffer (MMT), pH 9.0, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Resolution 3.00 Å R-free 0.243
6QSW Complement factor B protease domain in complex with the reversible inhibitor N-(2-bromo-4-methylnaphthalen-1-yl)-4,5-dihydro-1H-imidazol-2-amine. Deposited 2019-02-22 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain AAA 474–764（291 aa）
Not recorded SO4 SULFATE ION × 3 JGT ~{N}-(2-bromanyl-4-methyl-naphthalen-1-yl)-4,5-dihydro-1~{H}-imidazol-2-amine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；2.0 M ammonium sulfate, 0.1 M sodium acetate (pH 4.6), 2 mM inhibitor
Resolution 1.64 Å R-free 0.188
6QSW Complement factor B protease domain in complex with the reversible inhibitor N-(2-bromo-4-methylnaphthalen-1-yl)-4,5-dihydro-1H-imidazol-2-amine. Deposited 2019-02-22 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain BBB 474–764（291 aa）
Not recorded SO4 SULFATE ION × 4 JGT ~{N}-(2-bromanyl-4-methyl-naphthalen-1-yl)-4,5-dihydro-1~{H}-imidazol-2-amine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；2.0 M ammonium sulfate, 0.1 M sodium acetate (pH 4.6), 2 mM inhibitor
Resolution 1.64 Å R-free 0.188
6QSW Complement factor B protease domain in complex with the reversible inhibitor N-(2-bromo-4-methylnaphthalen-1-yl)-4,5-dihydro-1H-imidazol-2-amine. Deposited 2019-02-22 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain CCC 474–764（291 aa）
Not recorded SO4 SULFATE ION × 3 JGT ~{N}-(2-bromanyl-4-methyl-naphthalen-1-yl)-4,5-dihydro-1~{H}-imidazol-2-amine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；2.0 M ammonium sulfate, 0.1 M sodium acetate (pH 4.6), 2 mM inhibitor
Resolution 1.64 Å R-free 0.188
6QSX Complement 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. Deposited 2019-02-22 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain AAA 474–764（291 aa）
Not recorded SO4 SULFATE ION × 3 JGN [(2~{S},4~{S})-1-[(5,7-dimethyl-1~{H}-indol-4-yl)methyl]-4-methoxy-piperidin-2-yl]methanol × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；2.5 M ammonium sulfate, 0.1 mM sodium acetate (pH 4.6), 2 mM inhibitor
Resolution 1.77 Å R-free 0.220
6QSX Complement 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. Deposited 2019-02-22 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain BBB 474–764（291 aa）
Not recorded SO4 SULFATE ION × 4 JGN [(2~{S},4~{S})-1-[(5,7-dimethyl-1~{H}-indol-4-yl)methyl]-4-methoxy-piperidin-2-yl]methanol × 1 ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；2.5 M ammonium sulfate, 0.1 mM sodium acetate (pH 4.6), 2 mM inhibitor
Resolution 1.77 Å R-free 0.220
6RAV Complement factor B protease domain in complex with the reversible inhibitor 4-((2S,4S)-4-ethoxy-1-((5-methoxy-7-methyl-1H-indol-4-yl)methyl)piperidin-2-yl)benzoic acid Deposited 2019-04-08 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain AAA 474–764（291 aa）
Not recorded SO4 SULFATE ION × 2 JGQ 4-[(2~{S},4~{S})-4-ethoxy-1-[(5-methoxy-7-methyl-1~{H}-indol-4-yl)methyl]piperidin-2-yl]benzoic acid × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；24 % (w/v) PEG3350, 0.2 M ammonium acetate, 0.1 M Bis-Tris (pH 5.5), 2mM inhibitor
Resolution 1.70 Å R-free 0.227
6RAV Complement factor B protease domain in complex with the reversible inhibitor 4-((2S,4S)-4-ethoxy-1-((5-methoxy-7-methyl-1H-indol-4-yl)methyl)piperidin-2-yl)benzoic acid Deposited 2019-04-08 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain BBB 474–764（291 aa）
Not recorded SO4 SULFATE ION × 3 JGQ 4-[(2~{S},4~{S})-4-ethoxy-1-[(5-methoxy-7-methyl-1~{H}-indol-4-yl)methyl]piperidin-2-yl]benzoic acid × 1 ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；24 % (w/v) PEG3350, 0.2 M ammonium acetate, 0.1 M Bis-Tris (pH 5.5), 2mM inhibitor
Resolution 1.70 Å R-free 0.227
6RUR Structure of the SCIN stabilized C3bBb convertase bound to properdin Deposited 2019-05-29 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: dodecameric
Chain J 260–764（505 aa）
Chain L 260–764（505 aa）
Not recorded MAN alpha-D-mannopyranose × 18 MG MAGNESIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；277 K；50 mM MgAcetate 50 mM Mes 6.5 5 % w/v PEG 10K
Resolution 6.00 Å R-free 0.272
6RUV Structure of the SCIN stabilized C3bBb convertase bound to Properdin and a the non-inhibitory nanobody hFPNb1 Deposited 2019-05-29 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 14 PDB declaration: tetradecameric
Chain J 260–764（505 aa）
Chain L 260–764（505 aa）
Not recorded MAN alpha-D-mannopyranose × 21 MG MAGNESIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.8；277 K；100 mM NaCl, 5 % (w/v) PEG4000, 10 mM MgCl2, 100 mM Sodium Cacodylate trihydrate pH 5.8.
Resolution 6.15 Å R-free 0.271
6T8U Complement factor B in complex with 5-Bromo-3-chloro-N-(4,5-dihydro-1H-imidazol-2-yl)-7-methyl-1H-indol-4-amine Deposited 2019-10-25 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain AAA 474–764（291 aa）
Not recorded MVZ 5-bromanyl-3-chloranyl-~{N}-(1~{H}-imidazol-2-yl)-7-methyl-1~{H}-indol-4-amine × 1 SO4 SULFATE ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；298 K；2.4M AMMONIUM SULPHATE, 0.1 M SODIUM ACETATE PH 4.6
Resolution 2.84 Å R-free 0.239
6T8U Complement factor B in complex with 5-Bromo-3-chloro-N-(4,5-dihydro-1H-imidazol-2-yl)-7-methyl-1H-indol-4-amine Deposited 2019-10-25 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain BBB 474–764（291 aa）
Not recorded MVZ 5-bromanyl-3-chloranyl-~{N}-(1~{H}-imidazol-2-yl)-7-methyl-1~{H}-indol-4-amine × 1 SO4 SULFATE ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；298 K；2.4M AMMONIUM SULPHATE, 0.1 M SODIUM ACETATE PH 4.6
Resolution 2.84 Å R-free 0.239
6T8U Complement factor B in complex with 5-Bromo-3-chloro-N-(4,5-dihydro-1H-imidazol-2-yl)-7-methyl-1H-indol-4-amine Deposited 2019-10-25 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain CCC 474–764（291 aa）
Not recorded MVZ 5-bromanyl-3-chloranyl-~{N}-(1~{H}-imidazol-2-yl)-7-methyl-1~{H}-indol-4-amine × 1 SO4 SULFATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；298 K；2.4M AMMONIUM SULPHATE, 0.1 M SODIUM ACETATE PH 4.6
Resolution 2.84 Å R-free 0.239
6T8V Complement factor B in complex with (S)-5,7-Dimethyl-4-((2-phenylpiperidin-1-yl)methyl)-1H-indole Deposited 2019-10-25 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain AAA 474–764（291 aa）
Not recorded SO4 SULFATE ION × 2 MVK 4-[(2~{S})-1-[(5,7-dimethyl-1~{H}-indol-4-yl)methyl]piperidin-2-yl]benzoic acid × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；298 K；25% PEG3350, 0.1M HEPES PH 7.5, 5 mM inhibitor
Resolution 2.29 Å R-free 0.254
6T8V Complement factor B in complex with (S)-5,7-Dimethyl-4-((2-phenylpiperidin-1-yl)methyl)-1H-indole Deposited 2019-10-25 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain BBB 474–764（291 aa）
Not recorded SO4 SULFATE ION × 3 MVK 4-[(2~{S})-1-[(5,7-dimethyl-1~{H}-indol-4-yl)methyl]piperidin-2-yl]benzoic acid × 1 ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；298 K；25% PEG3350, 0.1M HEPES PH 7.5, 5 mM inhibitor
Resolution 2.29 Å R-free 0.254
6T8W Complement factor B in complex with (-)-4-(1-((5,7-Dimethyl-1H-indol-4-yl)methyl)piperidin-2-yl)benzoic acid Deposited 2019-10-25 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain AAA 474–764（291 aa）
Not recorded SO4 SULFATE ION × 2 MVW 5,7-dimethyl-4-[[(2~{S})-2-phenylpiperidin-1-yl]methyl]-1~{H}-indole × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；298 K；25% PEG3350, 0.1M BIS-TRIS PH 6.5, 0.2M AMMONIUM SULFATE, 0.1 MM ZNCL2, 1 mM inhibitor
Resolution 1.70 Å R-free 0.238
6T8W Complement factor B in complex with (-)-4-(1-((5,7-Dimethyl-1H-indol-4-yl)methyl)piperidin-2-yl)benzoic acid Deposited 2019-10-25 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain BBB 474–764（291 aa）
Not recorded SO4 SULFATE ION × 3 MVW 5,7-dimethyl-4-[[(2~{S})-2-phenylpiperidin-1-yl]methyl]-1~{H}-indole × 1 ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；298 K；25% PEG3350, 0.1M BIS-TRIS PH 6.5, 0.2M AMMONIUM SULFATE, 0.1 MM ZNCL2, 1 mM inhibitor
Resolution 1.70 Å R-free 0.238
7JTN Human Complement Factor B Inhibited by a Slow Off-Rate Modified Aptamer of 29 Bases Deposited 2020-08-18 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: dimeric
Chain A 1–764（764 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；0.1 M bis-tris, 0.2 M ammonium acetate, 25% peg-3350
Resolution 3.10 Å R-free 0.241
7JTN Human Complement Factor B Inhibited by a Slow Off-Rate Modified Aptamer of 29 Bases Deposited 2020-08-18 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein–DNA Monomer；Protein × 1 PDB declaration: dimeric
Chain C 1–764（764 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；0.1 M bis-tris, 0.2 M ammonium acetate, 25% peg-3350
Resolution 3.10 Å R-free 0.241
7JTQ Human Complement Factor B Inhibited by a Slow Off-Rate Modified Aptamer of 31 Bases Deposited 2020-08-18 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: dimeric
Chain A 1–764（764 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；0.1 M HEPES (pH 7.5), 0.2 M ammonium acetate, 25% (w/v) peg-3350
Resolution 3.50 Å R-free 0.257
7JTQ Human Complement Factor B Inhibited by a Slow Off-Rate Modified Aptamer of 31 Bases Deposited 2020-08-18 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein–DNA Monomer；Protein × 1 PDB declaration: dimeric
Chain C 1–764（764 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；0.1 M HEPES (pH 7.5), 0.2 M ammonium acetate, 25% (w/v) peg-3350
Resolution 3.50 Å R-free 0.257
7NOZ Structure of the nanobody stablized properdin bound alternative pathway proconvertase C3b:FB:FP Deposited 2021-02-26 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: hexameric
Chain F 35–764（730 aa）
Mutation：D279G MAN alpha-D-mannopyranose × 6 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.05 M Na-acetate pH 5.3, 0.1 M Mg-formate,7% PEG5000 MME
Resolution 3.90 Å R-free 0.265
8ENU Structure of the C3bB proconvertase in complex with lufaxin Deposited 2022-09-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric
Chain D 2–764（763 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.22 Å
8EOK Structure of the C3bB proconvertase in complex with lufaxin and factor Xa Deposited 2022-10-03 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: hexameric
Chain D 2–764（763 aa）
Not recorded MG MAGNESIUM ION × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.53 Å
8UIN Structure of the C3bBb-albicin complex Deposited 2023-10-10 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 8 PDB declaration: octameric
Chain J 260–487（228 aa）
Chain X 260–487（228 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4；10 mM Hepes pH 7.4, 150 mM NaCl, 5 mM MgCl2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.86 Å
9U62 AP pathways C3 convertase C3bBbP and C3 complex Deposited 2025-03-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: pentameric
Chain B 260–764（505 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5 NI NICKEL (II) ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.70 Å

25 other PDB entries and 44 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name CFAB_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–497； UniProt 268–764

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

SAXS profile for 1rtk

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1rtk
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1rtk
Deposition date deposition_date2003-12-10
Structure title titleCrystal Structure Analysis of the Bb segment of Factor B complexed with 4-guanidinobenzoic acid
Keywords keywordsfactor B, Bb, factor Bb-inhibitor complex, HORMONE-GROWTH FACTOR COMPLEX; HORMONE/GROWTH FACTOR
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier27.35 Å
Radius of gyration Rg (electron density) rg_electron26.71 Å
Forward intensity I(0) i048261000.00
Molecular weight molecular_weight54198.0 kDa
Excluded volume excluded_volume67806 ų
Envelope volume envelope_volume83256 ų
Hydration-shell volume shell_volume26807 ų
Envelope diameter envelope_diameter92.0 Å
Shell Rg shell_rg33.06 Å
Envelope Rg envelope_rg26.74 Å
Shape Rg shape_rg26.74 Å
Total Rg total_rg27.32 Å
Total atoms total_atoms3791
Residues n_residues486
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax89.5 Å
Rg (real space) rg_real27.48 Å
Rg uncertainty (real space) rg_real_error0.71 Å
I(0) (real space) i0_real4.8260e+07
I(0) uncertainty (real space) i0_real_error7.8510e+05
Rg (reciprocal space) rg_reciprocal27.44 Å
I(0) (reciprocal space) i0_reciprocal48260000.0000
Solution quality estimate total_estimate0.8739
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary27.8 Å
Skewness Skewness skewness0.432
Kurtosis Kurtosis kurtosis-0.477
Angular range angular_range— – 0.2900 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha9301000.0000
Real-space data points n_real_points59
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.830; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.941; Smooth: 0.925
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (6)

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7. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd1rtka1
Class classb — All beta proteins
Fold Fold foldb.47 — Trypsin-like serine proteases
Superfamily Superfamily superfamilyb.47.1 — Trypsin-like serine proteases
Family Family familyb.47.1.2 — Eukaryotic proteases
Domain ID domain_idd1rtka2
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.62 — vWA-like
Superfamily Superfamily superfamilyc.62.1 — vWA-like
Family Family familyc.62.1.1 — Integrin A (or I) domain

CATH v4.4 (3 domains)

Domain ID domain_id1rtkA01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily410 — von Willebrand factor, type A domain
Domain ID domain_id1rtkA02
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology10 — Thrombin, subunit H
Homologous superfamily homologous superfamily10 — Trypsin-like serine proteases
Domain ID domain_id1rtkA03
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology10 — Thrombin, subunit H
Homologous superfamily homologous superfamily10 — Trypsin-like serine proteases
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8. Citations (1)

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9. Files and Curves (10)