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- PDB-5f4l: HIV-1 gp120 complex with JP-III-048 -

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Basic information

Entry
Database: PDB / ID: 5f4l
TitleHIV-1 gp120 complex with JP-III-048
ComponentsENVELOPE GLYCOPROTEIN GP120 of HIV-1 clade C
KeywordsVIRAL PROTEIN / Crystal structure of HIV-1 gp120 complex with JP-III-048
Function / homology
Function and homology information


positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / virus-mediated perturbation of host defense response / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope ...positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / virus-mediated perturbation of host defense response / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane / structural molecule activity / plasma membrane
Similarity search - Function
HIV Envelope Protein Gp120; Chain G / Human immunodeficiency virus 1, Gp160, envelope glycoprotein / Envelope glycoprotein Gp160 / Retroviral envelope protein / Retroviral envelope protein GP41-like / Gp120 core superfamily / Envelope glycoprotein GP120 / Human immunodeficiency virus 1, envelope glycoprotein Gp120 / Beta Complex / Mainly Beta
Similarity search - Domain/homology
Chem-5VE / Envelope glycoprotein gp160
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.7 Å
AuthorsLiang, S. / Hendrickson, W.A.
CitationJournal: Acs Med.Chem.Lett. / Year: 2016
Title: Small-Molecule CD4-Mimics: Structure-Based Optimization of HIV-1 Entry Inhibition.
Authors: Melillo, B. / Liang, S. / Park, J. / Schon, A. / Courter, J.R. / LaLonde, J.M. / Wendler, D.J. / Princiotto, A.M. / Seaman, M.S. / Freire, E. / Sodroski, J. / Madani, N. / Hendrickson, W.A. / Smith, A.B.
History
DepositionDec 3, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 30, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Derived calculations / Refinement description / Category: pdbx_struct_oper_list / software
Item: _pdbx_struct_oper_list.symmetry_operation / _software.classification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ENVELOPE GLYCOPROTEIN GP120 of HIV-1 clade C
B: ENVELOPE GLYCOPROTEIN GP120 of HIV-1 clade C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,4874
Polymers77,5932
Non-polymers8942
Water1,13563
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area630 Å2
ΔGint-2 kcal/mol
Surface area30490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.159, 127.806, 192.470
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-615-

HOH

21B-619-

HOH

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Components

#1: Protein ENVELOPE GLYCOPROTEIN GP120 of HIV-1 clade C


Mass: 38796.527 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Cell line (production host): HEK 293 GnTi- cells / Production host: Homo sapiens (human) / References: UniProt: C6G099*PLUS
#2: Chemical ChemComp-5VE / ~{N}'-[(1~{R},2~{R})-2-(carbamimidamidomethyl)-6-(methylaminomethyl)-2,3-dihydro-1~{H}-inden-1-yl]-~{N}-(4-chloranyl-3-fluoranyl-phenyl)ethanediamide


Mass: 446.906 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H24ClFN6O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 63 / 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: 2.74 Å3/Da / Density % sol: 55.15 %
Crystal growTemperature: 290 K / Method: evaporation / Details: PEG 1500, magnesium chloride, imidazole

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Data collection

DiffractionMean temperature: 170 K
Diffraction sourceSource: SYNCHROTRON / Site: BSRF / Beamline: 1W2B / Wavelength: 0.9791 Å
DetectorType: APEX II CCD / Detector: CCD / Date: Apr 2, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.7→45.276 Å / Num. obs: 23229 / % possible obs: 99.9 % / Redundancy: 10.88 % / Rmerge(I) obs: 0.119 / Net I/σ(I): 12.5

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
XDSdata scaling
Aimlessdata scaling
PHASERphasing
RefinementResolution: 2.7→38.439 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 29 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2881 1134 4.89 %
Rwork0.2484 --
obs0.2503 23180 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.7→38.439 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5262 0 62 63 5387
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0045461
X-RAY DIFFRACTIONf_angle_d0.8117396
X-RAY DIFFRACTIONf_dihedral_angle_d13.4392018
X-RAY DIFFRACTIONf_chiral_restr0.032821
X-RAY DIFFRACTIONf_plane_restr0.004959
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7001-2.82290.3431100.32729X-RAY DIFFRACTION100
2.8229-2.97170.35751330.3032729X-RAY DIFFRACTION100
2.9717-3.15780.33841500.29722704X-RAY DIFFRACTION100
3.1578-3.40150.30551680.2712708X-RAY DIFFRACTION100
3.4015-3.74350.30081630.24332727X-RAY DIFFRACTION100
3.7435-4.28460.30311410.23562753X-RAY DIFFRACTION100
4.2846-5.39570.24571180.21292792X-RAY DIFFRACTION100
5.3957-38.44290.26091510.2482904X-RAY DIFFRACTION100

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