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

Method: X-RAY DIFFRACTION D_max: 90.2 Å Quality: EXCELLENT

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Complement factor B

Homo sapiens

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 AAA； UniProt 474–764	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
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain BBB； UniProt 474–764	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
3	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain CCC； UniProt 474–764	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

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 6T8U	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 mutation/modification 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 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 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
1RTK Crystal Structure Analysis of the Bb segment of Factor B complexed with 4-guanidinobenzoic acid Deposited 2003-12-10	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 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 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
2OK5 Human Complement factor B Deposited 2007-01-16	Different construct 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 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 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 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 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 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 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 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
6T8V Complement factor B in complex with (S)-5,7-Dimethyl-4-((2-phenylpiperidin-1-yl)methyl)-1H-indole Deposited 2019-10-25	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 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 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 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 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 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 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 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 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 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 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 42 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 AAA； PDBConstruct 1–291； UniProt 474–764 Author chain BBB； PDBConstruct 1–291； UniProt 474–764 Author chain CCC； PDBConstruct 1–291； UniProt 474–764

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

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	6t8u
Deposition date deposition_date	2019-10-25
Structure title title	Complement factor B in complex with 5-Bromo-3-chloro-N-(4,5-dihydro-1H-imidazol-2-yl)-7-methyl-1H-indol-4-amine
Keywords keywords	Complement immune, inhibitor, HYDROLASE; HYDROLASE
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	30.87 Å
Radius of gyration Rg (electron density) rg_electron	29.49 Å
Forward intensity I(0) i0	133582000.00
Molecular weight molecular_weight	91072.0 kDa
Excluded volume excluded_volume	113810 Å³
Envelope volume envelope_volume	144670 Å³
Hydration-shell volume shell_volume	39372 Å³
Envelope diameter envelope_diameter	93.6 Å
Shell Rg shell_rg	38.04 Å
Envelope Rg envelope_rg	29.36 Å
Shape Rg shape_rg	29.47 Å
Total Rg total_rg	30.34 Å
Total atoms total_atoms	6378
Residues n_residues	801
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	90.2 Å
Rg (real space) rg_real	30.66 Å
Rg uncertainty (real space) rg_real_error	0.47 Å
I(0) (real space) i0_real	1.3360e+08
I(0) uncertainty (real space) i0_real_error	1.7610e+06
Rg (reciprocal space) rg_reciprocal	30.75 Å
I(0) (reciprocal space) i0_reciprocal	133600000.0000
Solution quality estimate total_estimate	0.9123
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	44.2 Å
Skewness Skewness skewness	-0.006
Kurtosis Kurtosis kurtosis	-0.782
Angular range angular_range	— – 0.2550 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	44010000.0000
Real-space data points n_real_points	52
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.970; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.997; Smooth: 0.948

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Complement factor B
Molecular weight formula_weight	32955.9 kDa
EC 编号 ec_number	3.4.21.47
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	AAA,BBB,CCC
Atom count atom_count	6423

SLSLCGMVWEHRKGTDYHKQPWQAKISVIRPSKGHESCMGAVVSEYFVLTAAHCFTVDDKEHSIKVSVGGEKRDLEIEVVLFHPNYNINGKKEAGIPEFYDYDVALIKLKNKLKYGQTIRPICLPCTEGTTRALRLPPTTTCQQQKEELLPAQDIKALFVSEEEKKLTRKEVYIKNGDKKGSCERDAQYAPGYDKVKDISEVVTPRFLCTGGVSPYADPNTCRGDSGGPLIVHKRSRFIQVGVISWGVVDVCKNQKRQKQVPAHARDFHINLFQVLPWLKEKLQDEDLGFL

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	Human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Drosophila melanogaster

Entity 2 Entity 2 non-polymer

Description description	5-bromanyl-3-chloranyl-~{N}-(1~{H}-imidazol-2-yl)-7-methyl-1~{H}-indol-4-amine
Molecular weight formula_weight	325.6 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 3 Entity 3 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	8

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	45

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8. Citations (1)

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Unit-cell length a length_a	91.926 Å
Unit-cell length b length_b	91.926 Å
Unit-cell length c length_c	260.415 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	24

Space group space_group	P 43 21 2
Space-group number int_tables_number	96
Crystal system crystal_system	—

Resolution resolution	2.840 Å
Low-resolution limit resolution_low	86.684 Å
R factor r_factor	—
R_work r_work	0.1976
R_free r_free	0.2389

fit	/app/data/saxs_computation/t8/6t8u/6t8u.fit
pddf	/app/data/pr_computation/t8/6t8u/6t8u.pr.out
profile	/app/data/saxs_computation/t8/6t8u/6t8u.dat