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- PDB-8fly: HIV-1 gp120 complex with BNM-III-170 -

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Basic information

Entry
Database: PDB / ID: 8fly
TitleHIV-1 gp120 complex with BNM-III-170
ComponentsEnvelope glycoprotein gp120
KeywordsVIRAL PROTEIN/INHIBITOR / retrovirus / gp120 / entry inhibitor / structure-based drug design / small molecule / antiretroviral therapy / VIRAL PROTEIN-INHIBITOR complex
Function / homologyHIV Envelope Protein Gp120; Chain G / Human immunodeficiency virus 1, Gp160, envelope glycoprotein / Beta Complex / Mainly Beta / Chem-5VG
Function and homology information
Biological speciesHIV-1 06TG.HT008 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.04 Å
AuthorsGong, Z. / Hendrickson, W.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/Eunice Kennedy Shriver National Institute of Child Health & Human Development (NIH/NICHD)AI150471-25 8117 United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2023
Title: Indoline CD4-mimetic compounds mediate potent and broad HIV-1 inhibition and sensitization to antibody-dependent cellular cytotoxicity.
Authors: Fritschi, C.J. / Anang, S. / Gong, Z. / Mohammadi, M. / Richard, J. / Bourassa, C. / Severino, K.T. / Richter, H. / Yang, D. / Chen, H.C. / Chiu, T.J. / Seaman, M.S. / Madani, N. / Abrams, C. ...Authors: Fritschi, C.J. / Anang, S. / Gong, Z. / Mohammadi, M. / Richard, J. / Bourassa, C. / Severino, K.T. / Richter, H. / Yang, D. / Chen, H.C. / Chiu, T.J. / Seaman, M.S. / Madani, N. / Abrams, C. / Finzi, A. / Hendrickson, W.A. / Sodroski, J.G. / Smith III, A.B.
History
DepositionDec 22, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 5, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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
A: Envelope glycoprotein gp120
B: Envelope glycoprotein gp120
C: Envelope glycoprotein gp120
D: Envelope glycoprotein gp120
hetero molecules


Theoretical massNumber of molelcules
Total (without water)166,56234
Polymers159,0234
Non-polymers7,53930
Water3,531196
1
A: Envelope glycoprotein gp120
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,7519
Polymers39,7561
Non-polymers1,9958
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Envelope glycoprotein gp120
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,5308
Polymers39,7561
Non-polymers1,7747
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Envelope glycoprotein gp120
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,7519
Polymers39,7561
Non-polymers1,9958
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Envelope glycoprotein gp120
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,5308
Polymers39,7561
Non-polymers1,7747
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)71.790, 120.780, 194.900
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

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Components

#1: Protein
Envelope glycoprotein gp120


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: 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.: 26 / 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
#3: Chemical
ChemComp-5VG / ~{N}'-[(1~{R},2~{R})-2-(carbamimidamidomethyl)-5-(methylaminomethyl)-2,3-dihydro-1~{H}-inden-1-yl]-~{N}-(4-chloranyl-3-fluoranyl-phenyl)ethanediamide


Mass: 446.906 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H24ClFN6O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 196 / 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: 2.66 Å3/Da / Density % sol: 53.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 14 to 16 %(w/v) PEG 1500, 0.1 M CaCl2, 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: Dec 17, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.04→48.73 Å / Num. obs: 64404 / % possible obs: 94 % / Redundancy: 13.5 % / Biso Wilson estimate: 37.67 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.237 / Rpim(I) all: 0.067 / Net I/σ(I): 9.1
Reflection shellResolution: 2.04→2.34 Å / Rmerge(I) obs: 1.965 / Num. unique obs: 3788 / CC1/2: 0.534 / Rpim(I) all: 0.561 / % possible all: 74.8

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Processing

Software
NameVersionClassification
PHENIX1.20rc3_4406refinement
XDSdata reduction
STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.04→48.73 Å / SU ML: 0.2934 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 38.0666
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2761 1999 3.1 %
Rwork0.2473 62386 -
obs0.2482 64385 59.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 39.5 Å2
Refinement stepCycle: LAST / Resolution: 2.04→48.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10508 0 488 196 11192
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011311224
X-RAY DIFFRACTIONf_angle_d1.537415238
X-RAY DIFFRACTIONf_chiral_restr0.09441774
X-RAY DIFFRACTIONf_plane_restr0.02081938
X-RAY DIFFRACTIONf_dihedral_angle_d17.08671580
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.04-2.090.11630.36178X-RAY DIFFRACTION1.06
2.09-2.150.36120.3529412X-RAY DIFFRACTION5.57
2.15-2.210.3304250.3455755X-RAY DIFFRACTION10.27
2.21-2.290.3287380.31561205X-RAY DIFFRACTION16.27
2.29-2.370.3363580.33921801X-RAY DIFFRACTION24.35
2.37-2.460.3884840.34742616X-RAY DIFFRACTION35.14
2.46-2.570.29891300.32854043X-RAY DIFFRACTION54.43
2.57-2.710.33021970.32196180X-RAY DIFFRACTION83.5
2.71-2.880.33132370.30237363X-RAY DIFFRACTION98.65
2.88-3.10.3212390.28437460X-RAY DIFFRACTION100
3.1-3.410.31062400.26927512X-RAY DIFFRACTION99.97
3.41-3.910.27532400.23017510X-RAY DIFFRACTION99.99
3.91-4.920.23642440.20287583X-RAY DIFFRACTION99.97
4.92-48.730.22972520.21287868X-RAY DIFFRACTION99.8

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