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- PDB-7tjo: HIV-1 gp120 complex with CJF-II-197-S -

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Basic information

Entry
Database: PDB / ID: 7tjo
TitleHIV-1 gp120 complex with CJF-II-197-S
ComponentsGlycoprotein 120
KeywordsVIRUS / HIV gp120 entry inhibitor structure-based drug design X-ray crystallography antibody-dependent cellular cytotoxicity
Function / homologyChem-I6Q / IMIDAZOLE
Function and homology information
Biological speciesHIV-1 06TG.HT008 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.07 Å
AuthorsGong, Z. / Hendrickson, W.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)5P01AI150471-25 United States
CitationJournal: ACS Medicinal Chemistry Letters / Year: 2023
Title: Structural and Functional Characterization of Indane-Core CD4-Mimetic Compounds Substituted with Heterocyclic Amines
Authors: Chaplain, C. / Fritschi, C.J. / Anang, S. / Gong, Z. / Richard, J. / Bourassa, C. / Liang, S. / Mohammadi, M. / Park, J. / Finzi, A. / Madani, N. / Sodroski, J.G. / Abrams, C.F. / Hendrickson, W.A. / Smith, A.B.
History
DepositionJan 16, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 25, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
D: Glycoprotein 120
A: Glycoprotein 120
C: Glycoprotein 120
B: Glycoprotein 120
hetero molecules


Theoretical massNumber of molelcules
Total (without water)169,06345
Polymers159,0234
Non-polymers10,04141
Water1,20767
1
D: Glycoprotein 120
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,24911
Polymers39,7561
Non-polymers2,49310
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Glycoprotein 120
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,31812
Polymers39,7561
Non-polymers2,56211
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Glycoprotein 120
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,24911
Polymers39,7561
Non-polymers2,49310
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
B: Glycoprotein 120
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,24911
Polymers39,7561
Non-polymers2,49310
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)71.339, 121.826, 195.724
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1chain "A"
d_2ens_1chain "B"
d_3ens_1chain "D"
d_4ens_1chain "C"

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1LYSGLUB1 - 335
d_12ens_1I6QI6QO
d_21ens_1LYSGLUD1 - 335
d_22ens_1I6QI6QJA
d_31ens_1LYSGLUA1 - 335
d_32ens_1I6QI6QE
d_41ens_1LYSGLUC1 - 335
d_42ens_1I6QI6QZ

NCS oper:
IDCodeMatrixVector
1given(0.966347450711, 0.173617458707, -0.189814600432), (0.107652545013, -0.943109235047, -0.314572567655), (-0.23363119239, 0.283552374, -0.930061566318)-24.5483377336, -25.2679189826, -94.0807485641
2given(-0.99884146979, 0.0440419182169, 0.0193914328565), (0.042957830483, 0.997661539309, -0.0531608670372), (-0.0216873933114, -0.0522662646812, -0.998397663533)-32.9638325466, -2.04127018085, -95.0630397675
3given(0.967587255436, 0.0907885799821, -0.235653000962), (0.018104567221, -0.955679543578, -0.293851722187), (-0.251887132985, 0.280060785779, -0.926347034596)6.39654444091, 34.0816393718, -97.3232189849

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Components

#1: Protein
Glycoprotein 120


Mass: 39755.664 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HIV-1 06TG.HT008 (virus) / Production host: Homo sapiens (human)
#2: Chemical
ChemComp-I6Q / N~1~-[(1R,2R)-5-{[(3R)-3-aminopyrrolidin-1-yl]methyl}-2-(carbamimidamidomethyl)-2,3-dihydro-1H-inden-1-yl]-N~2~-(4-chloro-3-fluorophenyl)ethanediamide


Mass: 501.984 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: C24H29ClFN7O2
#3: 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.: 36 / Source method: obtained synthetically / 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
#4: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 67 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.83 Å3/Da / Density % sol: 56.57 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 14%(w/v) PEG 1500, 0.1 M calcium chloride, 0.1 M imidazole pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Oct 26, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 3.07→50 Å / Num. obs: 23992 / % possible obs: 99.8 % / Redundancy: 13.4 % / Biso Wilson estimate: 74.91 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.283 / Net I/σ(I): 8.4
Reflection shellResolution: 3.07→3.35 Å / Num. unique obs: 1200 / CC1/2: 0.664

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Processing

Software
NameVersionClassification
PHENIX1.20rc3_4406refinement
PHENIX1.20rc3_4406refinement
XDSdata reduction
STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3TGR

3tgr


Resolution: 3.07→48.93 Å / SU ML: 0.3926 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.4925
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2679 1997 8.33 %
Rwork0.2293 21971 -
obs0.2326 23968 73.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 64.61 Å2
Refinement stepCycle: LAST / Resolution: 3.07→48.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10508 0 649 67 11224
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.004211389
X-RAY DIFFRACTIONf_angle_d0.683115465
X-RAY DIFFRACTIONf_chiral_restr0.05531828
X-RAY DIFFRACTIONf_plane_restr0.0051949
X-RAY DIFFRACTIONf_dihedral_angle_d10.49421652
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2BX-RAY DIFFRACTIONNCS constraints3.15581624395E-13
ens_1d_3DX-RAY DIFFRACTIONNCS constraints1.92408701333E-13
ens_1d_4CX-RAY DIFFRACTIONNCS constraints4.41379579664E-13
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.07-3.150.3124100.3801105X-RAY DIFFRACTION5.03
3.15-3.230.4465270.3575300X-RAY DIFFRACTION14.32
3.23-3.330.333470.325519X-RAY DIFFRACTION25.04
3.33-3.430.3402760.2964834X-RAY DIFFRACTION39.33
3.44-3.560.33461230.30091352X-RAY DIFFRACTION64.1
3.56-3.70.2841530.27991673X-RAY DIFFRACTION79.49
3.7-3.870.30891830.272021X-RAY DIFFRACTION96.2
3.87-4.070.29771940.25042129X-RAY DIFFRACTION100
4.07-4.330.27981920.22762119X-RAY DIFFRACTION99.48
4.33-4.660.24221950.18872138X-RAY DIFFRACTION99.79
4.66-5.130.2641960.19052155X-RAY DIFFRACTION100
5.13-5.870.2711960.20292155X-RAY DIFFRACTION100
5.87-7.390.26571980.24332186X-RAY DIFFRACTION99.96
7.39-48.930.21942070.21432285X-RAY DIFFRACTION98.89

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