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- PDB-6fuj: Complement factor D in complex with the inhibitor N-(3'-(aminomet... -

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Basic information

Entry
Database: PDB / ID: 6fuj
TitleComplement factor D in complex with the inhibitor N-(3'-(aminomethyl)-[1,1'-biphenyl]-3-yl)-3-methylbutanamide
ComponentsComplement factor D
KeywordsHYDROLASE / SERINE PROTEASE / inhibitor / complex
Function / homology
Function and homology information


complement factor D / Alternative complement activation / complement activation / complement activation, alternative pathway / serine-type peptidase activity / protein maturation / platelet alpha granule lumen / response to bacterium / Platelet degranulation / secretory granule lumen ...complement factor D / Alternative complement activation / complement activation / complement activation, alternative pathway / serine-type peptidase activity / protein maturation / platelet alpha granule lumen / response to bacterium / Platelet degranulation / secretory granule lumen / ficolin-1-rich granule lumen / serine-type endopeptidase activity / Neutrophil degranulation / proteolysis / extracellular space / extracellular exosome / extracellular region
Similarity search - Function
Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Serine proteases, trypsin family, histidine active site. / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, serine active site. / Serine proteases, trypsin domain profile. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Trypsin-like serine proteases ...Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Serine proteases, trypsin family, histidine active site. / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, serine active site. / Serine proteases, trypsin domain profile. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Trypsin-like serine proteases / Thrombin, subunit H / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Chem-E8B / Complement factor D
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.25 Å
AuthorsMac Sweeney, A. / Ostermann, N. / Vulpetti, A. / Maibaum, J. / Erbel, P. / Lorthiois, E. / Yoon, T. / Randl, S. / Ruedisser, S.
CitationJournal: ACS Med Chem Lett / Year: 2018
Title: Discovery and Design of First Benzylamine-Based Ligands Binding to an Unlocked Conformation of the Complement Factor D.
Authors: Vulpetti, A. / Ostermann, N. / Randl, S. / Yoon, T. / Mac Sweeney, A. / Cumin, F. / Lorthiois, E. / Rudisser, S. / Erbel, P. / Maibaum, J.
History
DepositionFeb 27, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 6, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Complement factor D
B: Complement factor D
C: Complement factor D
D: Complement factor D
E: Complement factor D
F: Complement factor D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)149,2829
Polymers148,4356
Non-polymers8473
Water4,630257
1
A: Complement factor D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,0222
Polymers24,7391
Non-polymers2821
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Complement factor D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,0222
Polymers24,7391
Non-polymers2821
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Complement factor D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,0222
Polymers24,7391
Non-polymers2821
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Complement factor D


Theoretical massNumber of molelcules
Total (without water)24,7391
Polymers24,7391
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Complement factor D


Theoretical massNumber of molelcules
Total (without water)24,7391
Polymers24,7391
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Complement factor D


Theoretical massNumber of molelcules
Total (without water)24,7391
Polymers24,7391
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)116.662, 210.535, 143.521
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number21
Space group name H-MC222
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14A
24E
15A
25F
16B
26C
17B
27D
18B
28E
19B
29F
110C
210D
111C
211E
112C
212F
113D
213E
114D
214F
115E
215F

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: ILE / Beg label comp-ID: ILE / End auth comp-ID: ALA / End label comp-ID: ALA / Refine code: _ / Auth seq-ID: 16 - 243 / Label seq-ID: 1 - 228

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
12AA
22CC
13AA
23DD
14AA
24EE
15AA
25FF
16BB
26CC
17BB
27DD
18BB
28EE
19BB
29FF
110CC
210DD
111CC
211EE
112CC
212FF
113DD
213EE
114DD
214FF
115EE
215FF

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15

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Components

#1: Protein
Complement factor D / Adipsin / C3 convertase activator / Properdin factor D


Mass: 24739.121 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CFD, DF, PFD / Production host: Escherichia coli (E. coli) / References: UniProt: P00746, complement factor D
#2: Chemical ChemComp-E8B / ~{N}-[3-[3-(aminomethyl)phenyl]phenyl]-3-methyl-butanamide


Mass: 282.380 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C18H22N2O / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 257 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.97 Å3/Da / Density % sol: 58.57 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 22-25% PEG3350, 100 mM HEPES pH 7.5, 2 mM inhibitor

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Apr 20, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.25→83.05 Å / Num. obs: 83798 / % possible obs: 100 % / Redundancy: 6.14 % / Net I/σ(I): 10
Reflection shellResolution: 2.25→2.32 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementResolution: 2.25→71.76 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.912 / SU B: 8.421 / SU ML: 0.19 / Cross valid method: THROUGHOUT / ESU R: 0.268 / ESU R Free: 0.205 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24388 4190 5 %RANDOM
Rwork0.21761 ---
obs0.21892 79605 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 45.821 Å2
Baniso -1Baniso -2Baniso -3
1--0.12 Å2-0 Å20 Å2
2---0.2 Å2-0 Å2
3---0.31 Å2
Refinement stepCycle: 1 / Resolution: 2.25→71.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10234 0 63 257 10554
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.01910687
X-RAY DIFFRACTIONr_bond_other_d0.0020.029985
X-RAY DIFFRACTIONr_angle_refined_deg1.7871.97214576
X-RAY DIFFRACTIONr_angle_other_deg1.028323051
X-RAY DIFFRACTIONr_dihedral_angle_1_deg13.1245.21403
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.5522.494441
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.597151658
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.81615111
X-RAY DIFFRACTIONr_chiral_restr0.1020.21628
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02112343
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022174
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.9414.3865495
X-RAY DIFFRACTIONr_mcbond_other3.9354.3855494
X-RAY DIFFRACTIONr_mcangle_it6.2556.5666873
X-RAY DIFFRACTIONr_mcangle_other6.2556.5676874
X-RAY DIFFRACTIONr_scbond_it4.6544.9025191
X-RAY DIFFRACTIONr_scbond_other4.6534.9025192
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.2817.127699
X-RAY DIFFRACTIONr_long_range_B_refined9.96651.0310947
X-RAY DIFFRACTIONr_long_range_B_other9.97151.05610921
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A137900.06
12B137900.06
21A137360.06
22C137360.06
31A134000.09
32D134000.09
41A131600.08
42E131600.08
51A134280.09
52F134280.09
61B136700.04
62C136700.04
71B132820.08
72D132820.08
81B130480.08
82E130480.08
91B133360.09
92F133360.09
101C133020.08
102D133020.08
111C130500.07
112E130500.07
121C133420.08
122F133420.08
131D135400.05
132E135400.05
141D137360.06
142F137360.06
151E135560.06
152F135560.06
LS refinement shellResolution: 2.25→2.308 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.377 307 -
Rwork0.354 5841 -
obs--99.98 %

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