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- PDB-6aky: The Crystal structure of Human Chemokine Receptor CCR5 in complex... -

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Basic information

Entry
Database: PDB / ID: 6aky
TitleThe Crystal structure of Human Chemokine Receptor CCR5 in complex with compound 34
ComponentsC-C chemokine receptor type 5,Rubredoxin,C-C chemokine receptor type 5
KeywordsSIGNALING PROTEIN / G Protein-Coupled Receptor Chemokine Receptor CCR5 Antagonist Complex structure
Function / homology
Function and homology information


chemokine (C-C motif) ligand 5 binding / negative regulation of macrophage apoptotic process / signaling / chemokine receptor activity / C-C chemokine receptor activity / C-C chemokine binding / phosphatidylinositol phospholipase C activity / response to cholesterol / Chemokine receptors bind chemokines / release of sequestered calcium ion into cytosol by sarcoplasmic reticulum ...chemokine (C-C motif) ligand 5 binding / negative regulation of macrophage apoptotic process / signaling / chemokine receptor activity / C-C chemokine receptor activity / C-C chemokine binding / phosphatidylinositol phospholipase C activity / response to cholesterol / Chemokine receptors bind chemokines / release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / dendritic cell chemotaxis / Interleukin-10 signaling / Binding and entry of HIV virion / cellular defense response / coreceptor activity / cell chemotaxis / calcium-mediated signaling / chemotaxis / calcium ion transport / MAPK cascade / virus receptor activity / cell-cell signaling / actin binding / G alpha (i) signalling events / positive regulation of cytosolic calcium ion concentration / cellular response to lipopolysaccharide / electron transfer activity / cell surface receptor signaling pathway / endosome / immune response / inflammatory response / iron ion binding / G protein-coupled receptor signaling pathway / external side of plasma membrane / cell surface / identical protein binding / plasma membrane / cytoplasm
Similarity search - Function
CC chemokine receptor 5 / Rubredoxin / Rubredoxin, iron-binding site / Rubredoxin signature. / Chemokine receptor family / Rubredoxin domain / Rubredoxin / Rubredoxin-like domain / Rubredoxin-like domain profile. / G-protein coupled receptors family 1 signature. ...CC chemokine receptor 5 / Rubredoxin / Rubredoxin, iron-binding site / Rubredoxin signature. / Chemokine receptor family / Rubredoxin domain / Rubredoxin / Rubredoxin-like domain / Rubredoxin-like domain profile. / G-protein coupled receptors family 1 signature. / G protein-coupled receptor, rhodopsin-like / GPCR, rhodopsin-like, 7TM / G-protein coupled receptors family 1 profile. / 7 transmembrane receptor (rhodopsin family)
Similarity search - Domain/homology
Chem-A4X / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / Rubredoxin / C-C chemokine receptor type 5
Similarity search - Component
Biological speciesHomo sapiens (human)
Clostridium pasteurianum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsZhu, Y. / Zhao, Q. / Wu, B.
CitationJournal: J. Med. Chem. / Year: 2018
Title: Structure-Based Design of 1-Heteroaryl-1,3-propanediamine Derivatives as a Novel Series of CC-Chemokine Receptor 5 Antagonists.
Authors: Peng, P. / Chen, H. / Zhu, Y. / Wang, Z. / Li, J. / Luo, R.H. / Wang, J. / Chen, L. / Yang, L.M. / Jiang, H. / Xie, X. / Wu, B. / Zheng, Y.T. / Liu, H.
History
DepositionSep 4, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 24, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 21, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Nov 22, 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

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Assembly

Deposited unit
A: C-C chemokine receptor type 5,Rubredoxin,C-C chemokine receptor type 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,8184
Polymers43,8761
Non-polymers9423
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area18150 Å2
Unit cell
Length a, b, c (Å)35.585, 101.483, 136.569
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

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Components

#1: Protein C-C chemokine receptor type 5,Rubredoxin,C-C chemokine receptor type 5 / CCR5 / CHEMR13 / HIV-1 fusion coreceptor / Rd


Mass: 43876.227 Da / Num. of mol.: 1 / Mutation: C58Y, G163N, A233D, K303E
Source method: isolated from a genetically manipulated source
Details: Chimera protein of C-C chemokine receptor type 5 and Rubredoxin. Rubredoxin was inserted into CCR5 between residue 223 and 227.
Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Clostridium pasteurianum (bacteria)
Gene: CCR5, CMKBR5 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P51681, UniProt: P00268
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H40O4
#4: Chemical ChemComp-A4X / 4,4-difluoro-N-[(1S)-3-{(3-exo)-3-[3-methyl-5-(propan-2-yl)-4H-1,2,4-triazol-4-yl]-8-azabicyclo[3.2.1]octan-8-yl}-1-(thiophen-3-yl)propyl]cyclohexane-1-carboxamide


Mass: 519.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H39F2N5OS

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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: 2.59 Å3/Da / Density % sol: 52.6 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / Details: PEG400, HEPES, ammonium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 13, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 12438 / % possible obs: 96.7 % / Redundancy: 4 % / Biso Wilson estimate: 82.94 Å2 / Rpim(I) all: 0.069 / Net I/σ(I): 19
Reflection shellResolution: 2.8→2.9 Å / Num. unique obs: 2071 / Rpim(I) all: 0.576

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4MBS

4mbs


Resolution: 2.8→31.56 Å / Cor.coef. Fo:Fc: 0.905 / Cor.coef. Fo:Fc free: 0.912 / SU R Cruickshank DPI: 1.016 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 1.059 / SU Rfree Blow DPI: 0.37 / SU Rfree Cruickshank DPI: 0.373
RfactorNum. reflection% reflectionSelection details
Rfree0.283 639 5.15 %RANDOM
Rwork0.275 ---
obs0.275 12401 96.5 %-
Displacement parametersBiso mean: 82.89 Å2
Baniso -1Baniso -2Baniso -3
1-0.5437 Å20 Å20 Å2
2--2.9072 Å20 Å2
3----3.4509 Å2
Refine analyzeLuzzati coordinate error obs: 0.54 Å
Refinement stepCycle: 1 / Resolution: 2.8→31.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2657 0 49 0 2706
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.012779HARMONIC2
X-RAY DIFFRACTIONt_angle_deg13796HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d887SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes48HARMONIC2
X-RAY DIFFRACTIONt_gen_planes402HARMONIC5
X-RAY DIFFRACTIONt_it2779HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.05
X-RAY DIFFRACTIONt_other_torsion19.89
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion375SEMIHARMONIC5
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_contact3218SEMIHARMONIC4
LS refinement shellResolution: 2.8→3.07 Å / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.2919 163 5.69 %
Rwork0.2781 2700 -
all0.2789 2863 -
obs--95.59 %

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