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- PDB-5tcc: Complement Factor D inhibited with JH4 -

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Basic information

Entry
Database: PDB / ID: 5tcc
TitleComplement Factor D inhibited with JH4
ComponentsComplement factor DFactor D
KeywordsHYDROLASE/HYDROLASE INHIBITOR / serine protease / inhibitor / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


complement factor D / Alternative complement activation / complement activation, alternative pathway / complement activation / serine-type peptidase activity / platelet alpha granule lumen / response to bacterium / Platelet degranulation / secretory granule lumen / ficolin-1-rich granule lumen ...complement factor D / Alternative complement activation / complement activation, alternative pathway / complement activation / serine-type peptidase activity / 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 exosome / extracellular region
Similarity search - Function
Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, histidine active site. / Serine proteases, trypsin domain profile. / Serine proteases, trypsin family, serine active site. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Trypsin-like serine proteases ...Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, histidine active site. / Serine proteases, trypsin domain profile. / Serine proteases, trypsin family, serine active site. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / 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-J56 / Complement factor D
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.37 Å
AuthorsStuckey, J.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)P30CA046592 United States
CitationJournal: ACS Med Chem Lett / Year: 2016
Title: Buried Hydrogen Bond Interactions Contribute to the High Potency of Complement Factor D Inhibitors.
Authors: Yang, C.Y. / Phillips, J.G. / Stuckey, J.A. / Bai, L. / Sun, H. / Delproposto, J. / Brown, W.C. / Chinnaswamy, K.
History
DepositionSep 14, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 19, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 4, 2017Group: Database references
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)175,08916
Polymers171,0727
Non-polymers4,0179
Water0
1
A: Complement factor D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,8852
Polymers24,4391
Non-polymers4461
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Complement factor D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,8852
Polymers24,4391
Non-polymers4461
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Complement factor D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,3313
Polymers24,4391
Non-polymers8932
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Complement factor D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,8852
Polymers24,4391
Non-polymers4461
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: Complement factor D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,3313
Polymers24,4391
Non-polymers8932
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: Complement factor D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,8852
Polymers24,4391
Non-polymers4461
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
7
G: Complement factor D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,8852
Polymers24,4391
Non-polymers4461
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)98.886, 143.745, 346.166
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

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


Mass: 24438.807 Da / Num. of mol.: 7 / Fragment: residues 26-253
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CFD, DF, PFD / Production host: unidentified baculovirus / References: UniProt: P00746, complement factor D
#2: Chemical
ChemComp-J56 / (2S)-N-(6-bromopyridin-2-yl)-3-[(1H-indazol-1-yl)acetyl]-1,3-thiazolidine-2-carboxamide


Mass: 446.321 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C18H16BrN5O2S

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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: 3.6 Å3/Da / Density % sol: 65.79 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.1 M MES pH 6.5 and 25% PEG 8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 8, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 3.36→50 Å / Num. obs: 35335 / % possible obs: 100 % / Redundancy: 14.7 % / Biso Wilson estimate: 70.41 Å2 / Rmerge(I) obs: 0.102 / Rpim(I) all: 0.027 / Rrim(I) all: 0.105 / Χ2: 0.93 / Net I/av σ(I): 28.588 / Net I/σ(I): 8.5 / Num. measured all: 517784
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Diffraction-ID% possible all
3.36-3.42150.2590.9911100
3.42-3.4815.20.2390.9891100
3.48-3.5515.20.2060.9921100
3.55-3.6215.20.1790.9951100
3.62-3.715.20.1660.9941100
3.7-3.7815.10.1530.9951100
3.78-3.8815.10.1370.9961100
3.88-3.9815.10.1250.9971100
3.98-4.1150.1120.9971100
4.1-4.2314.80.0970.9971100
4.23-4.3814.70.0910.9971100
4.38-4.5614.50.0870.9981100
4.56-4.7714.40.0790.998199.9
4.77-5.0214.50.0720.998199.9
5.02-5.3314.60.0740.998199.9
5.33-5.7414.70.0770.9981100
5.74-6.3214.60.0820.9971100
6.32-7.2314.20.0830.9971100
7.23-9.113.70.0630.998199.8
9.1-5012.40.0330.999199.9

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Processing

Software
NameVersionClassification
HKL-2000data scaling
BUSTER-TNT2.10.2refinement
PDB_EXTRACT3.2data extraction
MOLREPphasing
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1BIO

1bio


Resolution: 3.37→49.86 Å / Cor.coef. Fo:Fc: 0.838 / Cor.coef. Fo:Fc free: 0.835 / Rfactor Rfree error: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.499
RfactorNum. reflection% reflectionSelection details
Rfree0.26 1761 5 %RANDOM
Rwork0.241 ---
obs0.242 35254 99.8 %-
Displacement parametersBiso max: 150.48 Å2 / Biso mean: 50.55 Å2 / Biso min: 9.57 Å2
Baniso -1Baniso -2Baniso -3
1--0.5609 Å20 Å20 Å2
2--1.0189 Å20 Å2
3----0.458 Å2
Refine analyzeLuzzati coordinate error obs: 0.48 Å
Refinement stepCycle: final / Resolution: 3.37→49.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11887 0 243 0 12130
Biso mean--67.43 --
Num. residues----1594
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d5634SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes265HARMONIC2
X-RAY DIFFRACTIONt_gen_planes2063HARMONIC5
X-RAY DIFFRACTIONt_it12429HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion1547SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact13738SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d12429HARMONIC20.008
X-RAY DIFFRACTIONt_angle_deg16963HARMONIC21.01
X-RAY DIFFRACTIONt_omega_torsion2.68
X-RAY DIFFRACTIONt_other_torsion2.94
LS refinement shellResolution: 3.37→3.47 Å / Total num. of bins used: 18
RfactorNum. reflection% reflection
Rfree0.334 140 5 %
Rwork0.252 2661 -
all-2801 -
obs--98.21 %

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