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- PDB-5tca: Complement Factor D inhibited with JH3 -

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Basic information

Entry
Database: PDB / ID: 5tca
TitleComplement Factor D inhibited with JH3
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-J55 / Complement factor D
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.15 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)175,48516
Polymers171,0727
Non-polymers4,4139
Water1,67593
1
A: Complement factor D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,9292
Polymers24,4391
Non-polymers4901
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Complement factor D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,9292
Polymers24,4391
Non-polymers4901
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Complement factor D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,4193
Polymers24,4391
Non-polymers9812
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Complement factor D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,4193
Polymers24,4391
Non-polymers9812
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: Complement factor D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,9292
Polymers24,4391
Non-polymers4901
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: Complement factor D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,9292
Polymers24,4391
Non-polymers4901
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
7
G: Complement factor D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,9292
Polymers24,4391
Non-polymers4901
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)99.361, 143.654, 347.592
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-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


Mass: 490.334 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C18H16BrN7O3S
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 93 / Source method: isolated from a natural source / Formula: H2O

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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: 3.63 Å3/Da / Density % sol: 66.07 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 0.1 M Tris-HCl pH 8.5, 15% PEG 20000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 4, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 3.15→50 Å / Num. obs: 43493 / % possible obs: 99.7 % / Redundancy: 14.9 % / Biso Wilson estimate: 82.46 Å2 / Rmerge(I) obs: 0.118 / Net I/av σ(I): 26.333 / Net I/σ(I): 6.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Diffraction-ID% possible all
3.15-3.2140.3470.983194.2
3.2-3.2615.10.3190.9871100
3.26-3.3315.20.2840.991100
3.33-3.3915.20.250.9921100
3.39-3.4715.20.2210.9941100
3.47-3.5515.10.1950.9941100
3.55-3.6415.10.1660.9951100
3.64-3.7315.10.1490.9961100
3.73-3.8415.10.1330.9971100
3.84-3.9715.10.1190.9971100
3.97-4.1115.10.1040.9981100
4.11-4.27150.0890.9981100
4.27-4.47150.0810.9981100
4.47-4.7150.0770.9981100
4.7-5150.0730.9981100
5-5.3814.90.0820.9981100
5.38-5.9314.80.0990.9971100
5.93-6.7814.70.1040.9951100
6.78-8.5414.50.080.9971100
8.54-5013.30.0380.999199.9

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Phasing

PhasingMethod: molecular replacement

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Processing

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

1bio


Resolution: 3.15→49.68 Å / Cor.coef. Fo:Fc: 0.875 / Cor.coef. Fo:Fc free: 0.829 / Rfactor Rfree error: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.431
RfactorNum. reflection% reflectionSelection details
Rfree0.264 2141 4.94 %RANDOM
Rwork0.225 ---
obs0.227 43361 99.7 %-
Displacement parametersBiso max: 133.63 Å2 / Biso mean: 51.48 Å2 / Biso min: 7.7 Å2
Baniso -1Baniso -2Baniso -3
1--1.4774 Å20 Å20 Å2
2--0.8988 Å20 Å2
3---0.5786 Å2
Refine analyzeLuzzati coordinate error obs: 0.42 Å
Refinement stepCycle: final / Resolution: 3.15→49.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11908 0 270 93 12271
Biso mean--52.35 34.24 -
Num. residues----1596
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d5656SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes266HARMONIC2
X-RAY DIFFRACTIONt_gen_planes2083HARMONIC5
X-RAY DIFFRACTIONt_it12478HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion1549SEMIHARMONIC5
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_contact14117SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d12478HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg17039HARMONIC21.11
X-RAY DIFFRACTIONt_omega_torsion3.08
X-RAY DIFFRACTIONt_other_torsion2.9
LS refinement shellResolution: 3.15→3.23 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.322 144 4.63 %
Rwork0.25 2967 -
all-3111 -
obs--97.23 %

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