6vmj

Crystal structure of human Complement Factor D with anti-Factor D Fab 20D12

Method: X-RAY DIFFRACTION D_max: 160.1 Å Quality: GOOD

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

Complement factor D

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 heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain Z； UniProt 26–253	Not recorded	Fab20D12 Light Chain × 1 Fab20D12 heavy chain × 1 CIT CITRIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；0.1 M sodium cacodylate pH 6.5, 1 M sodium citrate	Resolution 2.95 Å R-free 0.265
2	Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain Y； UniProt 26–253	Not recorded	Fab20D12 Light Chain × 1 Fab20D12 heavy chain × 1 CIT CITRIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；0.1 M sodium cacodylate pH 6.5, 1 M sodium citrate	Resolution 2.95 Å R-free 0.265
3	Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain X； UniProt 26–253	Not recorded	Fab20D12 Light Chain × 1 Fab20D12 heavy chain × 1 CIT CITRIC ACID × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；0.1 M sodium cacodylate pH 6.5, 1 M sodium citrate	Resolution 2.95 Å R-free 0.265
4	Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain W； UniProt 26–253	Not recorded	Fab20D12 Light Chain × 1 Fab20D12 heavy chain × 1 CIT CITRIC ACID × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；0.1 M sodium cacodylate pH 6.5, 1 M sodium citrate	Resolution 2.95 Å R-free 0.265

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 6VMJ	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1BIO HUMAN COMPLEMENT FACTOR D IN COMPLEX WITH ISATOIC ANHYDRIDE INHIBITOR Deposited 1998-06-18	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 26–253（228 aa）	Not recorded	SOA ISATOIC ANHYDRIDE × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.4；pH 6.4	Resolution 1.50 Å R-free 0.191
1DFP FACTOR D INHIBITED BY DIISOPROPYL FLUOROPHOSPHATE Deposited 1997-02-18	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 26–253（228 aa） Chain B 26–253（228 aa）	Not recorded	DFP DIISOPROPYL PHOSPHONATE × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.8；INHIBITED PROTEIN WAS CRYSTALLIZED FROM 12-16% PEG 6000 AND 0.2 M NACL,50MM MES BUFFER, PH=5.6-5.8.	Resolution 2.40 Å R-free 0.228
1DIC STRUCTURE OF 3,4-DICHLOROISOCOUMARIN-INHIBITED FACTOR D Deposited 1998-07-08	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 26–253（228 aa）	Not recorded	DIC 3,4-DICHLOROISOCOUMARIN × 1 O OXYGEN ATOM × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.6；pH 5.6	Resolution 1.80 Å R-free 0.251
1DST MUTANT OF FACTOR D WITH ENHANCED CATALYTIC ACTIVITY Deposited 1995-09-13	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 26–253（228 aa）	Mutation：S94Y, T214S, S215W	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.8；pH 6.8	Resolution 2.00 Å R-free 0.213
1DSU HUMAN FACTOR D, COMPLEMENT ACTIVATING ENZYME Deposited 1995-09-15	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 26–253（228 aa） Chain B 26–253（228 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.00 Å R-free 0.203
1FDP PROENZYME OF HUMAN COMPLEMENT FACTOR D, RECOMBINANT PROFACTOR D Deposited 1998-12-03	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 19–253（235 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.2；298 K；CRYSTALLIZATION CONDITIONS: THE RESERVOIR SOLUTION CONTAINED 10-12% PEG-6000 AND 30MM MES (PH5.2). THE DROPS CONTAINED EQUAL VOLUME OF RESERVOIR SOLUTION AND PROTEIN SOLUTION (10MG/ML), VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.10 Å R-free 0.251
1FDP PROENZYME OF HUMAN COMPLEMENT FACTOR D, RECOMBINANT PROFACTOR D Deposited 1998-12-03	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 19–253（235 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.2；298 K；CRYSTALLIZATION CONDITIONS: THE RESERVOIR SOLUTION CONTAINED 10-12% PEG-6000 AND 30MM MES (PH5.2). THE DROPS CONTAINED EQUAL VOLUME OF RESERVOIR SOLUTION AND PROTEIN SOLUTION (10MG/ML), VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.10 Å R-free 0.251
1FDP PROENZYME OF HUMAN COMPLEMENT FACTOR D, RECOMBINANT PROFACTOR D Deposited 1998-12-03	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 19–253（235 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.2；298 K；CRYSTALLIZATION CONDITIONS: THE RESERVOIR SOLUTION CONTAINED 10-12% PEG-6000 AND 30MM MES (PH5.2). THE DROPS CONTAINED EQUAL VOLUME OF RESERVOIR SOLUTION AND PROTEIN SOLUTION (10MG/ML), VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.10 Å R-free 0.251
1FDP PROENZYME OF HUMAN COMPLEMENT FACTOR D, RECOMBINANT PROFACTOR D Deposited 1998-12-03	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain D 19–253（235 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.2；298 K；CRYSTALLIZATION CONDITIONS: THE RESERVOIR SOLUTION CONTAINED 10-12% PEG-6000 AND 30MM MES (PH5.2). THE DROPS CONTAINED EQUAL VOLUME OF RESERVOIR SOLUTION AND PROTEIN SOLUTION (10MG/ML), VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.10 Å R-free 0.251
1HFD HUMAN COMPLEMENT FACTOR D IN A P21 CRYSTAL FORM Deposited 1998-06-18	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 26–253（228 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.4；pH 5.4	Resolution 2.30 Å R-free 0.216
2XW9 Crystal Structure of Complement Factor D mutant S183A Deposited 2010-11-01	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 26–253（228 aa）	Mutation：YES	GOL GLYCEROL × 4	X-RAY DIFFRACTION X-ray crystallization conditions pH 6；pH 6.0	Resolution 1.20 Å R-free 0.176
2XWA Crystal Structure of Complement Factor D Mutant R202A Deposited 2010-11-01	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 26–253（228 aa）	Mutation：YES	GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6；pH 6.0	Resolution 2.80 Å R-free 0.283
2XWA Crystal Structure of Complement Factor D Mutant R202A Deposited 2010-11-01	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 26–253（228 aa）	Mutation：YES	GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6；pH 6.0	Resolution 2.80 Å R-free 0.283
2XWB Crystal Structure of Complement C3b in complex with Factors B and D Deposited 2010-11-01	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 J 26–253（228 aa）	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 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 I 26–253（228 aa）	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 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 J 26–253（228 aa）	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 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 I 26–253（228 aa）	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
4CBN Crystal structure of Complement Factor D mutant R202A after conventional refinement Deposited 2013-10-15	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 26–253（228 aa） Fragment：RESIDUES 26-253	Mutation：YES	GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions 15% PEG 6000, 50 MM MES/NAOH, PH 6.0	Resolution 1.80 Å R-free 0.219
4CBN Crystal structure of Complement Factor D mutant R202A after conventional refinement Deposited 2013-10-15	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 26–253（228 aa） Fragment：RESIDUES 26-253	Mutation：YES	GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions 15% PEG 6000, 50 MM MES/NAOH, PH 6.0	Resolution 1.80 Å R-free 0.219
4CBO Crystal structure of Complement Factor D mutant R202A after ensemble refinement Deposited 2013-10-15	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 26–253（228 aa） Fragment：RESIDUES 26-253	Mutation：YES	GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions 15% PEG 6000, 50 MM MES/NAOH PH 6.0	Resolution 1.80 Å R-free 0.212
4CBO Crystal structure of Complement Factor D mutant R202A after ensemble refinement Deposited 2013-10-15	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 26–253（228 aa） Fragment：RESIDUES 26-253	Mutation：YES	GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions 15% PEG 6000, 50 MM MES/NAOH PH 6.0	Resolution 1.80 Å R-free 0.212
4D9R Inhibiting Alternative Pathway Complement Activation by Targeting the Exosite on Factor D Deposited 2012-01-11	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 26–253（228 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；277 K；0.1 M Tris-HCl, 0.02 M NH4PO4, MPD 50.0% v/v, 0.01 M hexamine cobalt (III) chloride, pH 8.5, vapor diffusion, hanging drop, temperature 277K	Resolution 2.42 Å R-free 0.251
4D9R Inhibiting Alternative Pathway Complement Activation by Targeting the Exosite on Factor D Deposited 2012-01-11	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 26–253（228 aa）	Not recorded	CL CHLORIDE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；277 K；0.1 M Tris-HCl, 0.02 M NH4PO4, MPD 50.0% v/v, 0.01 M hexamine cobalt (III) chloride, pH 8.5, vapor diffusion, hanging drop, temperature 277K	Resolution 2.42 Å R-free 0.251
5FBE COMPLEMENT FACTOR D IN COMPLEX WITH COMPOUND2 Deposited 2015-12-14	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 26–253（228 aa） Fragment：UNP residues 26-253	Not recorded	GOL GLYCEROL × 1 5W5 methyl 2-[[[(2~{S})-2-[[3-(trifluoromethyloxy)phenyl]carbamoyl]pyrrolidin-1-yl]carbonylamino]methyl]benzoate × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；1 MICROLITER PROTEIN SOLUTION WAS MIXED WITH 1 MICROLITER RESERVOIR SOLUTION. PROTEIN SOLUTION: 18 mg/mL FD, 10 mM Tris pH 7.0, 100 mM NaCl; RESERVOIR SOLUTION: 22% PEG3350, 100 mM HEPES pH 7.5; SOAKING AND CRYO: ADDITION of 10 mM COMPOUND2 for 45 min FOLLOWED by the ADDITION OF 0.5 MICROLITER GLYCEROL AND FLASH FREEZING IN LIQUIT NITROGEN.	Resolution 1.43 Å R-free 0.188
5FBI COMPLEMENT FACTOR D IN COMPLEX WITH COMPOUND 3b Deposited 2015-12-14	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 26–253（228 aa）	Not recorded	GOL GLYCEROL × 1 5WD 3-[(2-aminocarbonyl-1~{H}-indol-5-yl)oxymethyl]benzoic acid × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；1 Microliter of protein solution was mixed with 1 microliter of reservoir solution. Protein solution: 18.3 mg/ml factor D, 10 mM Tris pH 7.0, 100 mM sodium chloride; Reservoir solution: 22% PEG3350, 100 mM HEPES pH 7.5; Soaking and cryo: 0.5 ul 100 mM compound 3b in 90% DMSO was added to the crystal containing drop and incubated for 45 min followed by the addition of 0.5 ul glyerol and flash freezing in liquid nitrogen.	Resolution 1.47 Å R-free 0.196
5FCK COMPLEMENT FACTOR D IN COMPLEX WITH COMPOUND 5 Deposited 2015-12-15	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 26–253（228 aa）	Not recorded	5WC 1-[2-[(1~{R},3~{S},5~{R})-3-[[(1~{R})-1-(3-chloranyl-2-fluoranyl-phenyl)ethyl]carbamoyl]-2-azabicyclo[3.1.0]hexan-2-yl]-2-oxidanylidene-ethyl]pyrazolo[3,4-c]pyridine-3-carboxamide × 1 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；1 uL FD solution (18 mg/mL FD, 10 mM Tris pH 7.0, 100 mM NaCl) was mixed with 1 uL reservoir solution (25% PEG3350, 100 mM TRIS pH 8.0) and equilibrated against 1 mL reservoir solution.	Resolution 1.86 Å R-free 0.237
5MT0 COMPLEMENT FACTOR D IN COMPLEX WITH A REVERSIBLE INDOLE CARBOXYLIC ACID BASED INHIBITOR Deposited 2017-01-06	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 26–253（228 aa）	Not recorded	QJS 5-fluoranyl-3-[[(1~{S},2~{S})-2-phenylcyclopropyl]carbonylamino]-1~{H}-indole-2-carboxylic acid × 1 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；25% PEG3350, 100 mM BIS-TRIS pH 6.5	Resolution 1.29 Å R-free 0.196
5MT4 COMPLEMENT FACTOR D IN COMPLEX WITH A REVERSIBLE BENZOIC ACID BASED INHIBITOR Deposited 2017-01-06	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 26–253（228 aa）	Not recorded	M7O 2-[(phenylmethyl)carbamoylamino]benzoic acid × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；26% PEGME2000, 100mM Bis-Tris pH 6.5	Resolution 1.65 Å R-free 0.239
5NAR Complement factor D in complex with the inhibitor (S)-pyrrolidine-1,2-dicarboxylic acid 1-[(1-carbamoyl-1H-indol-3-yl)-amide] 2-[(3-trifluoromethoxy-phenyl)-amide] Deposited 2017-02-28	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 26–253（228 aa）	Not recorded	SO4 SULFATE ION × 1 8RW (2~{S})-~{N}1-(1-aminocarbonylindol-3-yl)-~{N}2-[3-(trifluoromethyloxy)phenyl]pyrrolidine-1,2-dicarboxamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；298 K；MM NACL, 0.5MM NVP-BVT244-NX-1 + 1 UL RESERVOIR SOLUTION	Resolution 1.55 Å R-free 0.231
5NAT Complement factor D in complex with the inhibitor (S)-Pyrrolidine-1,2-dicarboxylic acid 1-[(1-methyl-1H-indol-3-yl)-amide] 2-[(3-trifluoromethoxy-phenyl)-amide] Deposited 2017-02-28	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 26–253（228 aa）	Not recorded	GOL GLYCEROL × 2 8RT (2~{S})-~{N}1-(1-methylindol-3-yl)-~{N}2-[3-(trifluoromethyloxy)phenyl]pyrrolidine-1,2-dicarboxamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；298 K；MM NACL + 1 UL RESERVOIR SOLUTION	Resolution 1.17 Å
5NAW Complement factor D in complex with the inhibitor (1R,3S,5R)-2-Aza-bicyclo[3.1.0]hexane-2,3-dicarboxylic acid 2-[(1-carbamoyl-1H-indol-3-yl)-amide] 3-[(3-trifluoromethoxy-phenyl)-amide] Deposited 2017-02-28	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 26–253（228 aa）	Not recorded	8RZ (1~{R},3~{S},5~{R})-~{N}2-(1-aminocarbonylindol-3-yl)-~{N}3-[3-(trifluoromethyloxy)phenyl]-2-azabicyclo[3.1.0]hexane-2,3-dicarboxamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；298 K；27% PEG 3350 100 mM HEPES pH 7.5	Resolution 1.25 Å R-free 0.178
5NB6 Complement factor D in complex with the inhibitor (2S,4S)-4-Amino-pyrrolidine-1,2-dicarboxylic acid 1-[(1-carbamoyl-1H-indol-3-yl)-amide] 2-[(3-trifluoromethoxy-phenyl)-amide] Deposited 2017-03-01	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 26–253（228 aa）	Not recorded	8S2 (2~{S},4~{S})-~{N}1-(1-aminocarbonylindol-3-yl)-4-azanyl-~{N}2-[3-(trifluoromethyloxy)phenyl]pyrrolidine-1,2-dicarboxamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；298 K；22% PEG3350, 0.1 M HEPES pH 7.5, 50 mM NaCl	Resolution 1.75 Å R-free 0.297
5NB7 Complement factor D Deposited 2017-03-01	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 26–253（228 aa）	Not recorded	DMS DIMETHYL SULFOXIDE × 2 8NQ 1-[2-[(1~{R},3~{S},5~{R})-3-[(6-bromanylpyridin-2-yl)carbamoyl]-2-azabicyclo[3.1.0]hexan-2-yl]-2-oxidanylidene-ethyl]indazole-3-carboxamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；298 K；22% PEG 3350, 0.1 m HEPES pH 7.5, 50 mM NaCl	Resolution 1.33 Å R-free 0.196
5NBA Complement factor D in complex with the inhibitor (2S,4R)-4-Fluoro-pyrrolidine-1,2-dicarboxylic acid 1-[(1-carbamoyl-1H-indol-3-yl)-amide] 2-[(3-trifluoromethoxy-phenyl)-amide] Deposited 2017-03-01	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 26–253（228 aa）	Not recorded	8S5 (2~{S},4~{R})-~{N}1-(1-aminocarbonylindol-3-yl)-4-fluoranyl-~{N}2-[3-(trifluoromethyloxy)phenyl]pyrrolidine-1,2-dicarboxamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；23% PEG 3350, 0.1 M HEPES pH 7.5, 50 mM NaCl	Resolution 1.87 Å R-free 0.260
5TCA Complement Factor D inhibited with JH3 Deposited 2016-09-14	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 26–253（228 aa） Fragment：residues 26-253	Not recorded	J55 1-(2-{(2S)-2-[(6-bromopyridin-2-yl)carbamoyl]-1,3-thiazolidin-3-yl}-2-oxoethyl)-1H-pyrazolo[3,4-b]pyridine-3-carboxamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；0.1 M Tris-HCl pH 8.5, 15% PEG 20000	Resolution 3.15 Å R-free 0.264
5TCA Complement Factor D inhibited with JH3 Deposited 2016-09-14	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 26–253（228 aa） Fragment：residues 26-253	Not recorded	J55 1-(2-{(2S)-2-[(6-bromopyridin-2-yl)carbamoyl]-1,3-thiazolidin-3-yl}-2-oxoethyl)-1H-pyrazolo[3,4-b]pyridine-3-carboxamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；0.1 M Tris-HCl pH 8.5, 15% PEG 20000	Resolution 3.15 Å R-free 0.264
5TCA Complement Factor D inhibited with JH3 Deposited 2016-09-14	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 26–253（228 aa） Fragment：residues 26-253	Not recorded	J55 1-(2-{(2S)-2-[(6-bromopyridin-2-yl)carbamoyl]-1,3-thiazolidin-3-yl}-2-oxoethyl)-1H-pyrazolo[3,4-b]pyridine-3-carboxamide × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；0.1 M Tris-HCl pH 8.5, 15% PEG 20000	Resolution 3.15 Å R-free 0.264
5TCA Complement Factor D inhibited with JH3 Deposited 2016-09-14	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain D 26–253（228 aa） Fragment：residues 26-253	Not recorded	J55 1-(2-{(2S)-2-[(6-bromopyridin-2-yl)carbamoyl]-1,3-thiazolidin-3-yl}-2-oxoethyl)-1H-pyrazolo[3,4-b]pyridine-3-carboxamide × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；0.1 M Tris-HCl pH 8.5, 15% PEG 20000	Resolution 3.15 Å R-free 0.264
5TCA Complement Factor D inhibited with JH3 Deposited 2016-09-14	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 5 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain E 26–253（228 aa） Fragment：residues 26-253	Not recorded	J55 1-(2-{(2S)-2-[(6-bromopyridin-2-yl)carbamoyl]-1,3-thiazolidin-3-yl}-2-oxoethyl)-1H-pyrazolo[3,4-b]pyridine-3-carboxamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；0.1 M Tris-HCl pH 8.5, 15% PEG 20000	Resolution 3.15 Å R-free 0.264
5TCA Complement Factor D inhibited with JH3 Deposited 2016-09-14	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 6 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain F 26–253（228 aa） Fragment：residues 26-253	Not recorded	J55 1-(2-{(2S)-2-[(6-bromopyridin-2-yl)carbamoyl]-1,3-thiazolidin-3-yl}-2-oxoethyl)-1H-pyrazolo[3,4-b]pyridine-3-carboxamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；0.1 M Tris-HCl pH 8.5, 15% PEG 20000	Resolution 3.15 Å R-free 0.264
5TCA Complement Factor D inhibited with JH3 Deposited 2016-09-14	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 7 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain G 26–253（228 aa） Fragment：residues 26-253	Not recorded	J55 1-(2-{(2S)-2-[(6-bromopyridin-2-yl)carbamoyl]-1,3-thiazolidin-3-yl}-2-oxoethyl)-1H-pyrazolo[3,4-b]pyridine-3-carboxamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；0.1 M Tris-HCl pH 8.5, 15% PEG 20000	Resolution 3.15 Å R-free 0.264
5TCC Complement Factor D inhibited with JH4 Deposited 2016-09-14	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 26–253（228 aa） Fragment：residues 26-253	Not recorded	J56 (2S)-N-(6-bromopyridin-2-yl)-3-[(1H-indazol-1-yl)acetyl]-1,3-thiazolidine-2-carboxamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；0.1 M MES pH 6.5 and 25% PEG 8000	Resolution 3.37 Å R-free 0.260
5TCC Complement Factor D inhibited with JH4 Deposited 2016-09-14	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 26–253（228 aa） Fragment：residues 26-253	Not recorded	J56 (2S)-N-(6-bromopyridin-2-yl)-3-[(1H-indazol-1-yl)acetyl]-1,3-thiazolidine-2-carboxamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；0.1 M MES pH 6.5 and 25% PEG 8000	Resolution 3.37 Å R-free 0.260
5TCC Complement Factor D inhibited with JH4 Deposited 2016-09-14	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 26–253（228 aa） Fragment：residues 26-253	Not recorded	J56 (2S)-N-(6-bromopyridin-2-yl)-3-[(1H-indazol-1-yl)acetyl]-1,3-thiazolidine-2-carboxamide × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；0.1 M MES pH 6.5 and 25% PEG 8000	Resolution 3.37 Å R-free 0.260
5TCC Complement Factor D inhibited with JH4 Deposited 2016-09-14	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain D 26–253（228 aa） Fragment：residues 26-253	Not recorded	J56 (2S)-N-(6-bromopyridin-2-yl)-3-[(1H-indazol-1-yl)acetyl]-1,3-thiazolidine-2-carboxamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；0.1 M MES pH 6.5 and 25% PEG 8000	Resolution 3.37 Å R-free 0.260
5TCC Complement Factor D inhibited with JH4 Deposited 2016-09-14	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 5 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain E 26–253（228 aa） Fragment：residues 26-253	Not recorded	J56 (2S)-N-(6-bromopyridin-2-yl)-3-[(1H-indazol-1-yl)acetyl]-1,3-thiazolidine-2-carboxamide × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；0.1 M MES pH 6.5 and 25% PEG 8000	Resolution 3.37 Å R-free 0.260
5TCC Complement Factor D inhibited with JH4 Deposited 2016-09-14	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 6 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain F 26–253（228 aa） Fragment：residues 26-253	Not recorded	J56 (2S)-N-(6-bromopyridin-2-yl)-3-[(1H-indazol-1-yl)acetyl]-1,3-thiazolidine-2-carboxamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；0.1 M MES pH 6.5 and 25% PEG 8000	Resolution 3.37 Å R-free 0.260
5TCC Complement Factor D inhibited with JH4 Deposited 2016-09-14	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 7 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain G 26–253（228 aa） Fragment：residues 26-253	Not recorded	J56 (2S)-N-(6-bromopyridin-2-yl)-3-[(1H-indazol-1-yl)acetyl]-1,3-thiazolidine-2-carboxamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；0.1 M MES pH 6.5 and 25% PEG 8000	Resolution 3.37 Å R-free 0.260
6FTY COMPLEMENT FACTOR D COMPLEXED WITH COMPOUND 5 Deposited 2018-02-26	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 26–253（228 aa）	Not recorded	E7H 4-[[(5~{S},7~{R})-3-azanyl-1-adamantyl]carbonylamino]-1~{H}-indole-2-carboxamide × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；295 K；PEG 3350, 100 mM HEPES pH 7.5	Resolution 1.67 Å R-free 0.214
6FTZ COMPLEMENT FACTOR D COMPLEXED WITH COMPOUND 6 Deposited 2018-02-26	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 26–253（228 aa）	Not recorded	E7E ~{N}4-[3-(aminomethyl)phenyl]-1~{H}-indole-2,4-dicarboxamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；295 K；PEG3350, 100 mM HEPES pH 7.5	Resolution 1.67 Å R-free 0.220
6FUG Complement factor D in complex with the inhibitor 3-((3-((3-(aminomethyl)phenyl)amino)-1H-pyrazolo[3,4-d]pyrimidin-4-yl)amino)phenol Deposited 2018-02-27	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 26–253（228 aa）	Not recorded	E85 3-[[3-[[3-(aminomethyl)phenyl]amino]-1~{H}-pyrazolo[3,4-d]pyrimidin-4-yl]amino]phenol × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；25% PEG3350, 100 mM TRIS pH 8.5	Resolution 2.21 Å R-free 0.259
6FUG Complement factor D in complex with the inhibitor 3-((3-((3-(aminomethyl)phenyl)amino)-1H-pyrazolo[3,4-d]pyrimidin-4-yl)amino)phenol Deposited 2018-02-27	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 26–253（228 aa）	Not recorded	E85 3-[[3-[[3-(aminomethyl)phenyl]amino]-1~{H}-pyrazolo[3,4-d]pyrimidin-4-yl]amino]phenol × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；25% PEG3350, 100 mM TRIS pH 8.5	Resolution 2.21 Å R-free 0.259
6FUG Complement factor D in complex with the inhibitor 3-((3-((3-(aminomethyl)phenyl)amino)-1H-pyrazolo[3,4-d]pyrimidin-4-yl)amino)phenol Deposited 2018-02-27	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 26–253（228 aa）	Not recorded	E85 3-[[3-[[3-(aminomethyl)phenyl]amino]-1~{H}-pyrazolo[3,4-d]pyrimidin-4-yl]amino]phenol × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；25% PEG3350, 100 mM TRIS pH 8.5	Resolution 2.21 Å R-free 0.259
6FUG Complement factor D in complex with the inhibitor 3-((3-((3-(aminomethyl)phenyl)amino)-1H-pyrazolo[3,4-d]pyrimidin-4-yl)amino)phenol Deposited 2018-02-27	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain D 26–253（228 aa）	Not recorded	E85 3-[[3-[[3-(aminomethyl)phenyl]amino]-1~{H}-pyrazolo[3,4-d]pyrimidin-4-yl]amino]phenol × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；25% PEG3350, 100 mM TRIS pH 8.5	Resolution 2.21 Å R-free 0.259
6FUG Complement factor D in complex with the inhibitor 3-((3-((3-(aminomethyl)phenyl)amino)-1H-pyrazolo[3,4-d]pyrimidin-4-yl)amino)phenol Deposited 2018-02-27	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 5 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain E 26–253（228 aa）	Not recorded	E85 3-[[3-[[3-(aminomethyl)phenyl]amino]-1~{H}-pyrazolo[3,4-d]pyrimidin-4-yl]amino]phenol × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；25% PEG3350, 100 mM TRIS pH 8.5	Resolution 2.21 Å R-free 0.259
6FUG Complement factor D in complex with the inhibitor 3-((3-((3-(aminomethyl)phenyl)amino)-1H-pyrazolo[3,4-d]pyrimidin-4-yl)amino)phenol Deposited 2018-02-27	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 6 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain F 26–253（228 aa）	Not recorded	E85 3-[[3-[[3-(aminomethyl)phenyl]amino]-1~{H}-pyrazolo[3,4-d]pyrimidin-4-yl]amino]phenol × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；25% PEG3350, 100 mM TRIS pH 8.5	Resolution 2.21 Å R-free 0.259
6FUH Complement factor D in complex with the inhibitor (4-((3-(aminomethyl)phenyl)amino)quinazolin-2-yl)-L-valine Deposited 2018-02-27	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 26–253（228 aa）	Not recorded	E88 (2~{S})-2-[[4-[[3-(aminomethyl)phenyl]amino]quinazolin-2-yl]amino]-3-methyl-butanoic acid × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；25% PEG3350, 100 mM TRIS pH 8.5, 200 mM NH4SO2, 2 mM inhibitor	Resolution 1.37 Å R-free 0.180
6FUI Complement factor D in complex with the inhibitor 3-((3-((3-(aminomethyl)phenyl)amino)-1H-pyrazolo[3,4-d]pyrimidin-4-yl)amino)phenol Deposited 2018-02-27	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 26–253（228 aa）	Not recorded	E7W (1~{R},2~{S})-2-[[4-[[3-(aminomethyl)phenyl]amino]quinazolin-2-yl]amino]cyclohexane-1-carboxylic acid × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；22-25% PEG3350, 100 mM HEPES pH 7.5	Resolution 1.38 Å R-free 0.198
6FUJ Complement factor D in complex with the inhibitor N-(3'-(aminomethyl)-[1,1'-biphenyl]-3-yl)-3-methylbutanamide Deposited 2018-02-27	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 26–253（228 aa）	Not recorded	E8B ~{N}-[3-[3-(aminomethyl)phenyl]phenyl]-3-methyl-butanamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；22-25% PEG3350, 100 mM HEPES pH 7.5, 2 mM inhibitor	Resolution 2.25 Å R-free 0.244
6FUJ Complement factor D in complex with the inhibitor N-(3'-(aminomethyl)-[1,1'-biphenyl]-3-yl)-3-methylbutanamide Deposited 2018-02-27	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 26–253（228 aa）	Not recorded	E8B ~{N}-[3-[3-(aminomethyl)phenyl]phenyl]-3-methyl-butanamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；22-25% PEG3350, 100 mM HEPES pH 7.5, 2 mM inhibitor	Resolution 2.25 Å R-free 0.244
6FUJ Complement factor D in complex with the inhibitor N-(3'-(aminomethyl)-[1,1'-biphenyl]-3-yl)-3-methylbutanamide Deposited 2018-02-27	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 26–253（228 aa）	Not recorded	E8B ~{N}-[3-[3-(aminomethyl)phenyl]phenyl]-3-methyl-butanamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；22-25% PEG3350, 100 mM HEPES pH 7.5, 2 mM inhibitor	Resolution 2.25 Å R-free 0.244
6FUJ Complement factor D in complex with the inhibitor N-(3'-(aminomethyl)-[1,1'-biphenyl]-3-yl)-3-methylbutanamide Deposited 2018-02-27	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain D 26–253（228 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；22-25% PEG3350, 100 mM HEPES pH 7.5, 2 mM inhibitor	Resolution 2.25 Å R-free 0.244
6FUJ Complement factor D in complex with the inhibitor N-(3'-(aminomethyl)-[1,1'-biphenyl]-3-yl)-3-methylbutanamide Deposited 2018-02-27	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 5 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain E 26–253（228 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；22-25% PEG3350, 100 mM HEPES pH 7.5, 2 mM inhibitor	Resolution 2.25 Å R-free 0.244
6FUJ Complement factor D in complex with the inhibitor N-(3'-(aminomethyl)-[1,1'-biphenyl]-3-yl)-3-methylbutanamide Deposited 2018-02-27	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 6 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain F 26–253（228 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；22-25% PEG3350, 100 mM HEPES pH 7.5, 2 mM inhibitor	Resolution 2.25 Å R-free 0.244
6FUT Complement factor D in complex with the inhibitor (S)-3'-(aminomethyl)-N-(1,2,3,4-tetrahydronaphthalen-1-yl)-[1,1'-biphenyl]-3-carboxamide Deposited 2018-02-27	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 26–253（228 aa）	Not recorded	E82 3-[3-(aminomethyl)phenyl]-~{N}-[(1~{S})-1,2,3,4-tetrahydronaphthalen-1-yl]benzamide × 1 SIN SUCCINIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；22-25% PEG3350, 100 mM HEPES pH 7.5	Resolution 1.50 Å R-free 0.184
6QMR Complement factor D in complex with the inhibitor (S)-2-(2-((3'-(1-amino-2-hydroxyethyl)-[1,1'-biphenyl]-3-yl)methoxy)phenyl)acetic acid Deposited 2019-02-08	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2–253（252 aa）	Not recorded	J6T 2-[2-[[3-[3-[(1~{S})-1-azanyl-2-oxidanyl-ethyl]phenyl]phenyl]methoxy]phenyl]ethanoic acid × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；30% PEG MME 2000, 0.1M sodium thiocyanate	Resolution 2.00 Å R-free 0.256
6QMR Complement factor D in complex with the inhibitor (S)-2-(2-((3'-(1-amino-2-hydroxyethyl)-[1,1'-biphenyl]-3-yl)methoxy)phenyl)acetic acid Deposited 2019-02-08	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 2–253（252 aa）	Not recorded	J6T 2-[2-[[3-[3-[(1~{S})-1-azanyl-2-oxidanyl-ethyl]phenyl]phenyl]methoxy]phenyl]ethanoic acid × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；30% PEG MME 2000, 0.1M sodium thiocyanate	Resolution 2.00 Å R-free 0.256
6QMR Complement factor D in complex with the inhibitor (S)-2-(2-((3'-(1-amino-2-hydroxyethyl)-[1,1'-biphenyl]-3-yl)methoxy)phenyl)acetic acid Deposited 2019-02-08	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 2–253（252 aa）	Not recorded	J6T 2-[2-[[3-[3-[(1~{S})-1-azanyl-2-oxidanyl-ethyl]phenyl]phenyl]methoxy]phenyl]ethanoic acid × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；30% PEG MME 2000, 0.1M sodium thiocyanate	Resolution 2.00 Å R-free 0.256
6QMR Complement factor D in complex with the inhibitor (S)-2-(2-((3'-(1-amino-2-hydroxyethyl)-[1,1'-biphenyl]-3-yl)methoxy)phenyl)acetic acid Deposited 2019-02-08	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain D 2–253（252 aa）	Not recorded	J6T 2-[2-[[3-[3-[(1~{S})-1-azanyl-2-oxidanyl-ethyl]phenyl]phenyl]methoxy]phenyl]ethanoic acid × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；30% PEG MME 2000, 0.1M sodium thiocyanate	Resolution 2.00 Å R-free 0.256
6QMR Complement factor D in complex with the inhibitor (S)-2-(2-((3'-(1-amino-2-hydroxyethyl)-[1,1'-biphenyl]-3-yl)methoxy)phenyl)acetic acid Deposited 2019-02-08	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 5 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain E 2–253（252 aa）	Not recorded	J6T 2-[2-[[3-[3-[(1~{S})-1-azanyl-2-oxidanyl-ethyl]phenyl]phenyl]methoxy]phenyl]ethanoic acid × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；30% PEG MME 2000, 0.1M sodium thiocyanate	Resolution 2.00 Å R-free 0.256
6QMR Complement factor D in complex with the inhibitor (S)-2-(2-((3'-(1-amino-2-hydroxyethyl)-[1,1'-biphenyl]-3-yl)methoxy)phenyl)acetic acid Deposited 2019-02-08	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 6 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain F 2–253（252 aa）	Not recorded	J6T 2-[2-[[3-[3-[(1~{S})-1-azanyl-2-oxidanyl-ethyl]phenyl]phenyl]methoxy]phenyl]ethanoic acid × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；30% PEG MME 2000, 0.1M sodium thiocyanate	Resolution 2.00 Å R-free 0.256
6QMT Complement factor D in complex with the inhibitor 2-(2-(3'-(aminomethyl)-[1,1'-biphenyl]-3-carboxamido)phenyl)acetic acid Deposited 2019-02-08	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2–253（252 aa）	Not recorded	J7B 2-[2-[[3-[3-(aminomethyl)phenyl]phenyl]carbonylamino]phenyl]ethanoic acid × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；293 K；25% PEGME 3350, 100 mM Bis-Tris pH 5.5	Resolution 1.80 Å R-free 0.231
6QMT Complement factor D in complex with the inhibitor 2-(2-(3'-(aminomethyl)-[1,1'-biphenyl]-3-carboxamido)phenyl)acetic acid Deposited 2019-02-08	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 2–253（252 aa）	Not recorded	J7B 2-[2-[[3-[3-(aminomethyl)phenyl]phenyl]carbonylamino]phenyl]ethanoic acid × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；293 K；25% PEGME 3350, 100 mM Bis-Tris pH 5.5	Resolution 1.80 Å R-free 0.231
6VMK Crystal structure of human Complement Factor D with anti-Factor D Fab 20D12 Deposited 2020-01-28	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain W 26–253（228 aa）	Not recorded	GOL GLYCEROL × 1 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；277 K；0.1 M sodium citrate pH 5.0, 8% PEG 8000	Resolution 3.01 Å R-free 0.215
6VMK Crystal structure of human Complement Factor D with anti-Factor D Fab 20D12 Deposited 2020-01-28	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 10 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain d 26–253（228 aa）	Not recorded	GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；277 K；0.1 M sodium citrate pH 5.0, 8% PEG 8000	Resolution 3.01 Å R-free 0.215
6VMK Crystal structure of human Complement Factor D with anti-Factor D Fab 20D12 Deposited 2020-01-28	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 11 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain g 26–253（228 aa）	Not recorded	GOL GLYCEROL × 1 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；277 K；0.1 M sodium citrate pH 5.0, 8% PEG 8000	Resolution 3.01 Å R-free 0.215
6VMK Crystal structure of human Complement Factor D with anti-Factor D Fab 20D12 Deposited 2020-01-28	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 12 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain j 26–253（228 aa）	Not recorded	GOL GLYCEROL × 1 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；277 K；0.1 M sodium citrate pH 5.0, 8% PEG 8000	Resolution 3.01 Å R-free 0.215
6VMK Crystal structure of human Complement Factor D with anti-Factor D Fab 20D12 Deposited 2020-01-28	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 13 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain m 26–253（228 aa）	Not recorded	GOL GLYCEROL × 1 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；277 K；0.1 M sodium citrate pH 5.0, 8% PEG 8000	Resolution 3.01 Å R-free 0.215
6VMK Crystal structure of human Complement Factor D with anti-Factor D Fab 20D12 Deposited 2020-01-28	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 14 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain p 26–253（228 aa）	Not recorded	GOL GLYCEROL × 1 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；277 K；0.1 M sodium citrate pH 5.0, 8% PEG 8000	Resolution 3.01 Å R-free 0.215
6VMK Crystal structure of human Complement Factor D with anti-Factor D Fab 20D12 Deposited 2020-01-28	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 15 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain s 26–253（228 aa）	Not recorded	GOL GLYCEROL × 1 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；277 K；0.1 M sodium citrate pH 5.0, 8% PEG 8000	Resolution 3.01 Å R-free 0.215
6VMK Crystal structure of human Complement Factor D with anti-Factor D Fab 20D12 Deposited 2020-01-28	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 16 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain v 26–253（228 aa）	Not recorded	GOL GLYCEROL × 1 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；277 K；0.1 M sodium citrate pH 5.0, 8% PEG 8000	Resolution 3.01 Å R-free 0.215
6VMK Crystal structure of human Complement Factor D with anti-Factor D Fab 20D12 Deposited 2020-01-28	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 26–253（228 aa）	Not recorded	GOL GLYCEROL × 1 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；277 K；0.1 M sodium citrate pH 5.0, 8% PEG 8000	Resolution 3.01 Å R-free 0.215
6VMK Crystal structure of human Complement Factor D with anti-Factor D Fab 20D12 Deposited 2020-01-28	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain F 26–253（228 aa）	Not recorded	GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；277 K；0.1 M sodium citrate pH 5.0, 8% PEG 8000	Resolution 3.01 Å R-free 0.215
6VMK Crystal structure of human Complement Factor D with anti-Factor D Fab 20D12 Deposited 2020-01-28	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain I 26–253（228 aa）	Not recorded	GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；277 K；0.1 M sodium citrate pH 5.0, 8% PEG 8000	Resolution 3.01 Å R-free 0.215
6VMK Crystal structure of human Complement Factor D with anti-Factor D Fab 20D12 Deposited 2020-01-28	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 5 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain N 26–253（228 aa）	Not recorded	GOL GLYCEROL × 1 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；277 K；0.1 M sodium citrate pH 5.0, 8% PEG 8000	Resolution 3.01 Å R-free 0.215
6VMK Crystal structure of human Complement Factor D with anti-Factor D Fab 20D12 Deposited 2020-01-28	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 6 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain Q 26–253（228 aa）	Not recorded	GOL GLYCEROL × 1 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；277 K；0.1 M sodium citrate pH 5.0, 8% PEG 8000	Resolution 3.01 Å R-free 0.215
6VMK Crystal structure of human Complement Factor D with anti-Factor D Fab 20D12 Deposited 2020-01-28	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 7 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain T 26–253（228 aa）	Not recorded	GOL GLYCEROL × 1 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；277 K；0.1 M sodium citrate pH 5.0, 8% PEG 8000	Resolution 3.01 Å R-free 0.215
6VMK Crystal structure of human Complement Factor D with anti-Factor D Fab 20D12 Deposited 2020-01-28	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 8 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain X 26–253（228 aa）	Not recorded	GOL GLYCEROL × 1 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；277 K；0.1 M sodium citrate pH 5.0, 8% PEG 8000	Resolution 3.01 Å R-free 0.215
6VMK Crystal structure of human Complement Factor D with anti-Factor D Fab 20D12 Deposited 2020-01-28	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 9 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain a 26–253（228 aa）	Not recorded	GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；277 K；0.1 M sodium citrate pH 5.0, 8% PEG 8000	Resolution 3.01 Å R-free 0.215
8D95 Scaffold Hopping via Ring Opening Enables Identification of Acyclic Compounds as New Complement Factor D Inhibitors Deposited 2022-06-09	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 26–253（228 aa）	Not recorded	QIE N-(6-bromopyridin-2-yl)-1-[(3-cyanophenyl)acetyl]-L-prolinamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.8；300 K；PEG 6k	Resolution 2.17 Å R-free 0.263
8DEA Scaffold Hopping via Ring Opening Enables Identification of Acyclic Compounds as New Complement Factor D Inhibitors Deposited 2022-06-20	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 26–253（228 aa）	Not recorded	R7X 1-[(3-acetylphenyl)acetyl]-N-(6-bromopyridin-2-yl)-L-prolinamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.8；293 K；peg4k 25% , 0.1M MES 5.8 buffer	Resolution 2.21 Å R-free 0.300
8DEA Scaffold Hopping via Ring Opening Enables Identification of Acyclic Compounds as New Complement Factor D Inhibitors Deposited 2022-06-20	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 26–253（228 aa）	Not recorded	R7X 1-[(3-acetylphenyl)acetyl]-N-(6-bromopyridin-2-yl)-L-prolinamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.8；293 K；peg4k 25% , 0.1M MES 5.8 buffer	Resolution 2.21 Å R-free 0.300
8DEA Scaffold Hopping via Ring Opening Enables Identification of Acyclic Compounds as New Complement Factor D Inhibitors Deposited 2022-06-20	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 26–253（228 aa）	Not recorded	R7X 1-[(3-acetylphenyl)acetyl]-N-(6-bromopyridin-2-yl)-L-prolinamide × 1 GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.8；293 K；peg4k 25% , 0.1M MES 5.8 buffer	Resolution 2.21 Å R-free 0.300
8DEA Scaffold Hopping via Ring Opening Enables Identification of Acyclic Compounds as New Complement Factor D Inhibitors Deposited 2022-06-20	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain D 26–253（228 aa）	Not recorded	R7X 1-[(3-acetylphenyl)acetyl]-N-(6-bromopyridin-2-yl)-L-prolinamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.8；293 K；peg4k 25% , 0.1M MES 5.8 buffer	Resolution 2.21 Å R-free 0.300
8DG6 Scaffold Hopping via Ring Opening Enables Identification of Acyclic Compounds as New Complement Factor D Inhibitors Deposited 2022-06-23	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 26–253（228 aa）	Not recorded	S7X 1-{2-[(2S)-2-{[(3-chloro-2-fluorophenyl)methyl]carbamoyl}pyrrolidin-1-yl]-2-oxoethyl}-1H-indazole-3-carboxamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.8；300 K；peg4k 20-30%	Resolution 1.99 Å R-free 0.251

39 other PDB entries and 95 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	CFAD_HUMAN
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain W； PDBConstruct 1–228； UniProt 26–253 Author chain X； PDBConstruct 1–228； UniProt 26–253 Author chain Y； PDBConstruct 1–228； UniProt 26–253 Author chain Z； PDBConstruct 1–228； UniProt 26–253

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	6vmj
Deposition date deposition_date	2020-01-28
Structure title title	Crystal structure of human Complement Factor D with anti-Factor D Fab 20D12
Keywords keywords	CFD, Factor D, Fab, HYDROLASE, HYDROLASE-IMMUNE SYSTEM complex; HYDROLASE/IMMUNE SYSTEM
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	49.27 Å
Radius of gyration Rg (electron density) rg_electron	49.55 Å
Forward intensity I(0) i0	1215400000.00
Molecular weight molecular_weight	281170.0 kDa
Excluded volume excluded_volume	348920 Å³
Envelope volume envelope_volume	507750 Å³
Hydration-shell volume shell_volume	87648 Å³
Envelope diameter envelope_diameter	169.6 Å
Shell Rg shell_rg	51.21 Å
Envelope Rg envelope_rg	49.09 Å
Shape Rg shape_rg	49.54 Å
Total Rg total_rg	49.63 Å
Total atoms total_atoms	19777
Residues n_residues	2562
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	160.1 Å
Rg (real space) rg_real	49.18 Å
Rg uncertainty (real space) rg_real_error	1.31 Å
I(0) (real space) i0_real	1.2150e+09
I(0) uncertainty (real space) i0_real_error	2.2610e+07
Rg (reciprocal space) rg_reciprocal	49.27 Å
I(0) (reciprocal space) i0_reciprocal	1216000000.0000
Solution quality estimate total_estimate	0.8783
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	55.0 Å
Skewness Skewness skewness	0.284
Kurtosis Kurtosis kurtosis	-0.347
Angular range angular_range	— – 0.1600 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	50220000.0000
Real-space data points n_real_points	33
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.881; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.992; Smooth: 0.779

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	Fab20D12 Light Chain
Molecular weight formula_weight	23360.8 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,E,I,L
Atom count atom_count	19932

DIQMTQSPSSLSASVGDRVTITCKASQNVDTDVAWFQQKPGKAPKGLIYSASSRYSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCQQYNNYPLTFGQGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

来源 Source

来源生物 organism	Homo sapiens
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Fab20D12 heavy chain
Molecular weight formula_weight	23668.4 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,F,J,M

EVQLVQSGAEVKKPGASVKVSCKASGYTFTSYYMYWVRQAPGQGLEWIGEINPTSGGTNFNEKFKSRATLTVDTSTSTAYLELSSLRSEDTAVYYCAREGGFAYWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKTHT

来源 Source

来源生物 organism	Homo sapiens
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Entity 3 Entity 3 polymer

Description description	Complement factor D
Molecular weight formula_weight	24438.8 kDa
EC 编号 ec_number	3.4.21.46
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	W,X,Y,Z

ILGGREAEAHARPYMASVQLNGAHLCGGVLVAEQWVLSAAHCLEDAADGKVQVLLGAHSLSQPEPSKRLYDVLRAVPHPDSQPDTIDHDLLLLQLSEKATLGPAVRPLPWQRVDRDVAPGTLCDVAGWGIVNHAGRRPDSLQHVLLPVLDRATCNRRTHHDGAITERLMCAESNRRDSCKGDSGGPLVCGGVLEGVVTSGSRVCGNRKKPGIYTRVASYAAWIDSVLA

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	Cricetulus griseus

Entity 4 Entity 4 non-polymer

Description description	CITRIC ACID
Molecular weight formula_weight	192.1 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	151

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7. Fold Classification (SCOP + CATH) 32 domains

SCOP 2.08 (16 domains)

Domain ID domain_id	d6vmja1
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.0 — automated matches

Domain ID domain_id	d6vmja2
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.2 — C1 set domains (antibody constant domain-like)

Domain ID domain_id	d6vmjb_
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.0 — automated matches

Domain ID domain_id	d6vmje1
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.0 — automated matches

Domain ID domain_id	d6vmje2
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.2 — C1 set domains (antibody constant domain-like)

Domain ID domain_id	d6vmjf_
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.0 — automated matches

Domain ID domain_id	d6vmji1
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.0 — automated matches

Domain ID domain_id	d6vmji2
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.2 — C1 set domains (antibody constant domain-like)

Domain ID domain_id	d6vmjj_
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.0 — automated matches

Domain ID domain_id	d6vmjl1
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.0 — automated matches

Domain ID domain_id	d6vmjl2
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.2 — C1 set domains (antibody constant domain-like)

Domain ID domain_id	d6vmjm_
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.0 — automated matches

Domain ID domain_id	d6vmjw_
Class class	b — All beta proteins
Fold Fold fold	b.47 — Trypsin-like serine proteases
Superfamily Superfamily superfamily	b.47.1 — Trypsin-like serine proteases
Family Family family	b.47.1.2 — Eukaryotic proteases

Domain ID domain_id	d6vmjx_
Class class	b — All beta proteins
Fold Fold fold	b.47 — Trypsin-like serine proteases
Superfamily Superfamily superfamily	b.47.1 — Trypsin-like serine proteases
Family Family family	b.47.1.2 — Eukaryotic proteases

Domain ID domain_id	d6vmjy_
Class class	b — All beta proteins
Fold Fold fold	b.47 — Trypsin-like serine proteases
Superfamily Superfamily superfamily	b.47.1 — Trypsin-like serine proteases
Family Family family	b.47.1.2 — Eukaryotic proteases

Domain ID domain_id	d6vmjz_
Class class	b — All beta proteins
Fold Fold fold	b.47 — Trypsin-like serine proteases
Superfamily Superfamily superfamily	b.47.1 — Trypsin-like serine proteases
Family Family family	b.47.1.2 — Eukaryotic proteases

CATH v4.4 (16 domains)

Domain ID domain_id	6vmjA01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	6vmjA02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	6vmjB01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	6vmjB02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	6vmjE01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	6vmjE02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	6vmjF01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	6vmjF02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	6vmjI01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	6vmjI02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	6vmjJ01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	6vmjJ02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	6vmjL01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	6vmjL02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	6vmjM01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	6vmjM02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

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8. Citations (1)

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Unit-cell length a length_a	180.843 Å
Unit-cell length b length_b	180.843 Å
Unit-cell length c length_c	304.189 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	32

Space group space_group	P 41 21 2
Space-group number int_tables_number	92
Crystal system crystal_system	—

Resolution resolution	2.950 Å
Low-resolution limit resolution_low	47.240 Å
R factor r_factor	0.2180
R_work r_work	0.2175
R_free r_free	0.2652

Crystal structure of human Complement Factor D with anti-Factor D Fab 20D12

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

Complement factor D

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

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

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

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 polymer

Polymer Polymer

来源 Source

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

7. Fold Classification (SCOP + CATH) 32 domains

SCOP 2.08 (16 domains)

CATH v4.4 (16 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

fit	/app/data/saxs_computation/vm/6vmj/6vmj.fit
pddf	/app/data/pr_computation/vm/6vmj/6vmj.pr.out
profile	/app/data/saxs_computation/vm/6vmj/6vmj.dat