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

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Basic information

Entry
Database: PDB / ID: 6akx
TitleThe Crystal structure of Human Chemokine Receptor CCR5 in complex with compound 21
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 / alkane catabolic process / C-C chemokine receptor activity / C-C chemokine binding / phosphatidylinositol phospholipase C activity / response to cholesterol / Chemokine receptors bind chemokines ...chemokine (C-C motif) ligand 5 binding / negative regulation of macrophage apoptotic process / signaling / chemokine receptor activity / alkane catabolic process / C-C chemokine receptor activity / C-C chemokine binding / phosphatidylinositol phospholipase C activity / response to cholesterol / Chemokine receptors bind chemokines / dendritic cell chemotaxis / release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / 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 / cell-cell signaling / virus receptor activity / actin binding / positive regulation of cytosolic calcium ion concentration / G alpha (i) signalling events / cellular response to lipopolysaccharide / electron transfer activity / cell surface receptor signaling pathway / endosome / inflammatory response / immune 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. ...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-A4R / NITRATE ION / 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
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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
B: C-C chemokine receptor type 5,Rubredoxin,C-C chemokine receptor type 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,9478
Polymers87,7522
Non-polymers1,1946
Water181
1
A: C-C chemokine receptor type 5,Rubredoxin,C-C chemokine receptor type 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,4734
Polymers43,8761
Non-polymers5973
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area17740 Å2
MethodPISA
2
B: C-C chemokine receptor type 5,Rubredoxin,C-C chemokine receptor type 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,4734
Polymers43,8761
Non-polymers5973
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10 Å2
ΔGint-2 kcal/mol
Surface area18210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.640, 102.740, 136.870
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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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.: 2 / 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.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: NO3
#4: Chemical ChemComp-A4R / 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-2-yl)propyl]cyclopentanecarboxamide


Mass: 469.686 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C26H39N5OS
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / 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: 2.69 Å3/Da / Density % sol: 54.23 %
Crystal growTemperature: 293.15 K / Method: lipidic cubic phase / Details: PEG 400, HEPES pH 7.5, 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: Jul 20, 2014
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: 25389 / % possible obs: 98.1 % / Redundancy: 5 % / Biso Wilson estimate: 69.51 Å2 / Rsym value: 0.186 / Net I/σ(I): 5.7
Reflection shellResolution: 2.8→2.9 Å / Num. unique obs: 2587 / Rsym value: 0.723

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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→29.66 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.893 / SU R Cruickshank DPI: 0.776 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.722 / SU Rfree Blow DPI: 0.344 / SU Rfree Cruickshank DPI: 0.352
RfactorNum. reflection% reflectionSelection details
Rfree0.269 1297 5.11 %RANDOM
Rwork0.213 ---
obs0.216 25389 98.2 %-
Displacement parametersBiso mean: 64.87 Å2
Baniso -1Baniso -2Baniso -3
1-6.5034 Å20 Å20 Å2
2---16.5479 Å20 Å2
3---10.0445 Å2
Refine analyzeLuzzati coordinate error obs: 0.41 Å
Refinement stepCycle: 1 / Resolution: 2.8→29.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5450 0 76 1 5527
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.015684HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.187756HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1840SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes102HARMONIC2
X-RAY DIFFRACTIONt_gen_planes825HARMONIC5
X-RAY DIFFRACTIONt_it5684HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.47
X-RAY DIFFRACTIONt_other_torsion20.64
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion750SEMIHARMONIC5
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_contact6671SEMIHARMONIC4
LS refinement shellResolution: 2.8→2.91 Å / Total num. of bins used: 13
RfactorNum. reflection% reflection
Rfree0.2591 139 5.13 %
Rwork0.2083 2569 -
all0.2108 2708 -
obs--94.14 %

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