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- PDB-8fm5: HIV-1 gp120 complex with DY-III-065 -

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Basic information

Entry
Database: PDB / ID: 8fm5
TitleHIV-1 gp120 complex with DY-III-065
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-Y2E
Function and homology information
Biological speciesHIV-1 06TG.HT008 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.88 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

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Assembly

Deposited unit
D: Envelope glycoprotein gp120
A: Envelope glycoprotein gp120
C: Envelope glycoprotein gp120
B: Envelope glycoprotein gp120
hetero molecules


Theoretical massNumber of molelcules
Total (without water)167,12634
Polymers159,0234
Non-polymers8,10330
Water3,765209
1
D: Envelope glycoprotein gp120
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,6718
Polymers39,7561
Non-polymers1,9157
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Envelope glycoprotein gp120
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,8929
Polymers39,7561
Non-polymers2,1368
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Envelope glycoprotein gp120
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,8929
Polymers39,7561
Non-polymers2,1368
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
B: Envelope glycoprotein gp120
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,6718
Polymers39,7561
Non-polymers1,9157
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)71.520, 121.660, 195.230
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-Y2E / 3,3,3-trifluoropropyl (2R,3S)-2-(carbamimidamidomethyl)-3-[2-(4-chloro-3-fluoroanilino)(oxo)acetamido]-6-[(methylamino)methyl]-2,3-dihydro-1H-indole-1-carboxylate


Mass: 587.954 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C24H26ClF4N7O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 209 / 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: 2.67 Å3/Da / Density % sol: 53.94 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 14% to 16% (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-E / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Nov 12, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.88→48.81 Å / Num. obs: 88049 / % possible obs: 93.7 % / Redundancy: 11.9 % / Biso Wilson estimate: 30.52 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.177 / Rpim(I) all: 0.052 / Net I/σ(I): 11.9
Reflection shellResolution: 1.88→2.12 Å / Rmerge(I) obs: 1.666 / Num. unique obs: 4402 / CC1/2: 0.567 / Rpim(I) all: 0.514

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Processing

Software
NameVersionClassification
PHENIX1.20rc3_4406refinement
XDSdata reduction
STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.88→48.81 Å / SU ML: 0.2991 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 39.6872
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2876 2000 2.27 %
Rwork0.2672 86034 -
obs0.2676 88034 63.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 50.13 Å2
Refinement stepCycle: LAST / Resolution: 1.88→48.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10508 0 524 209 11241
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012411260
X-RAY DIFFRACTIONf_angle_d2.388315294
X-RAY DIFFRACTIONf_chiral_restr0.14331774
X-RAY DIFFRACTIONf_plane_restr0.03731942
X-RAY DIFFRACTIONf_dihedral_angle_d18.98051600
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.88-1.930.554450.4421218X-RAY DIFFRACTION2.3
1.93-1.980.3159150.3499655X-RAY DIFFRACTION6.91
1.98-2.040.3622260.34641135X-RAY DIFFRACTION11.85
2.04-2.110.3755450.35971883X-RAY DIFFRACTION19.75
2.11-2.180.3377760.35233311X-RAY DIFFRACTION34.79
2.18-2.270.33111120.33984765X-RAY DIFFRACTION49.8
2.27-2.370.37071550.33936711X-RAY DIFFRACTION69.98
2.37-2.50.39272050.35128820X-RAY DIFFRACTION92.09
2.5-2.650.36072240.33479632X-RAY DIFFRACTION99.96
2.65-2.860.32272240.31549641X-RAY DIFFRACTION99.98
2.86-3.150.32892250.29959646X-RAY DIFFRACTION99.98
3.15-3.60.32572260.26689716X-RAY DIFFRACTION99.98
3.6-4.540.2412270.21699783X-RAY DIFFRACTION99.96
4.54-48.810.20272350.207910118X-RAY DIFFRACTION99.88

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