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- PDB-5f4u: HIV-1 gp120 complex with BNM-IV-197 -

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Basic information

Entry
Database: PDB / ID: 5f4u
TitleHIV-1 gp120 complex with BNM-IV-197
ComponentsENVELOPE GLYCOPROTEIN GP120 of HIV-1 clade C
KeywordsVIRAL PROTEIN / gp120
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 / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / fusion of virus membrane with host plasma membrane / virus-mediated perturbation of host defense response / 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 / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / fusion of virus membrane with host plasma membrane / virus-mediated perturbation of host defense response / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / apoptotic process / host cell plasma membrane / structural molecule activity / virion membrane / 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-5VH / Envelope glycoprotein gp160
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 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
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)81,44717
Polymers77,5932
Non-polymers3,85415
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4710 Å2
ΔGint53 kcal/mol
Surface area31740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.439, 128.123, 193.599
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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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: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 13
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical ChemComp-5VH / ~{N}'-[(1~{R},2~{R})-2-(carbamimidamidomethyl)-6-[[carbamimidoyl(methyl)amino]methyl]-2,3-dihydro-1~{H}-inden-1-yl]-~{N}-(4-chloranyl-3-fluoranyl-phenyl)ethanediamide


Mass: 488.946 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C22H26ClFN8O2
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: 2.7 Å3/Da / Density % sol: 54.49 %
Crystal growTemperature: 290 K / Method: evaporation / Details: peg 1500,calcium chloride, imidazole

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Data collection

DiffractionMean temperature: 180 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 12, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 3.1→48.4 Å / Num. obs: 15645 / % possible obs: 99.9 % / Redundancy: 5.88 % / Rmerge(I) obs: 0.133 / Net I/σ(I): 9

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
XDSdata scaling
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3TGR

3tgr


Resolution: 3.1→48.4 Å / SU ML: 0.43 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.84 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2799 804 5.15 %
Rwork0.2176 --
obs0.2208 15610 99.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.1→48.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5262 0 250 0 5512
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0055649
X-RAY DIFFRACTIONf_angle_d1.1757653
X-RAY DIFFRACTIONf_dihedral_angle_d15.112048
X-RAY DIFFRACTIONf_chiral_restr0.065877
X-RAY DIFFRACTIONf_plane_restr0.005972
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1-3.29420.33341540.27312407X-RAY DIFFRACTION100
3.2942-3.54850.35811360.2452436X-RAY DIFFRACTION100
3.5485-3.90540.3277970.22072461X-RAY DIFFRACTION100
3.9054-4.47020.27371390.20362464X-RAY DIFFRACTION100
4.4702-5.63070.24131260.20162492X-RAY DIFFRACTION100
5.6307-48.40560.26841520.2182546X-RAY DIFFRACTION99

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