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- PDB-7rsx: HIV-1 gp120 complex with CJF-III-049-S -

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Basic information

Entry
Database: PDB / ID: 7rsx
TitleHIV-1 gp120 complex with CJF-III-049-S
ComponentsENVELOPE GLYCOPROTEIN GP120
KeywordsVIRAL PROTEIN / HIV-1 gp120 / inhibitor
Function / homologyChem-7IT
Function and homology information
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsLiang, S. / Hendrickson, W.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P41GM116799 United States
CitationJournal: Acs Med.Chem.Lett. / Year: 2021
Title: Identification of gp120 Residue His105 as a Novel Target for HIV-1 Neutralization by Small-Molecule CD4-Mimics.
Authors: Fritschi, C.J. / Liang, S. / Mohammadi, M. / Anang, S. / Moraca, F. / Chen, J. / Madani, N. / Sodroski, J.G. / Abrams, C.F. / Hendrickson, W.A. / Smith 3rd, A.B.
History
DepositionAug 12, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 8, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: ENVELOPE GLYCOPROTEIN GP120
B: ENVELOPE GLYCOPROTEIN GP120
A: ENVELOPE GLYCOPROTEIN GP120
D: ENVELOPE GLYCOPROTEIN GP120
hetero molecules


Theoretical massNumber of molelcules
Total (without water)169,14733
Polymers161,4774
Non-polymers7,67029
Water95553
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)71.812, 120.661, 195.247
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
ENVELOPE GLYCOPROTEIN GP120


Mass: 40369.281 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Production host: Homo sapiens (human)
#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.: 25 / Source method: obtained synthetically / Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
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-7IT / N~1~-{(1R,2R,3S)-2-(carbamimidamidomethyl)-3-[(3S)-3,4-dihydroxybutyl]-5-[(methylamino)methyl]-2,3-dihydro-1H-inden-1-yl}-N~2~-(4-chloro-3-fluorophenyl)ethanediamide


Mass: 535.011 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C25H32ClFN6O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 53 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.81 Å3/Da / Density % sol: 56.16 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop
Details: 23% (w/v) PEG 1500, 0.1 M CaCl2, 0.1 M imidazole pH 6.5

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Data collection

DiffractionMean temperature: 77 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 6, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.75→67.4 Å / Num. obs: 44923 / % possible obs: 99.8 % / Redundancy: 10.39 % / CC1/2: 0.995 / Rmerge(I) obs: 0.159 / Net I/σ(I): 10.5
Reflection shellResolution: 2.75→2.85 Å / Rmerge(I) obs: 0.999 / Num. unique obs: 4332 / CC1/2: 0.802

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Processing

Software
NameVersionClassification
PHENIX1.14refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3TGR

3tgr


Resolution: 2.75→67.398 Å / SU ML: 0.42 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 31.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2814 2187 4.88 %
Rwork0.2396 --
obs0.2417 44819 99.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 133.05 Å2 / Biso mean: 65.0263 Å2 / Biso min: 29.98 Å2
Refinement stepCycle: final / Resolution: 2.75→67.398 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10508 0 498 53 11059
Biso mean--76.12 56.26 -
Num. residues----1340

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