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- PDB-5bn0: A new HIV fusion peptide inhibitor -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 5bn0
TitleA new HIV fusion peptide inhibitor
Components
  • (Envelope glycoprotein gp160) x 2
  • Envelope glycoprotein
KeywordsVIRAL PROTEIN / Inhibitor
Function / homology
Function and homology information


Synthesis and processing of ENV and VPU / symbiont-mediated evasion of host immune response / positive regulation of establishment of T cell polarity / Alpha-defensins / Dectin-2 family / Binding and entry of HIV virion / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / actin filament organization / host cell endosome membrane ...Synthesis and processing of ENV and VPU / symbiont-mediated evasion of host immune response / positive regulation of establishment of T cell polarity / Alpha-defensins / Dectin-2 family / Binding and entry of HIV virion / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / actin filament organization / host cell endosome membrane / Assembly Of The HIV Virion / Budding and maturation of HIV virion / clathrin-dependent endocytosis of virus by host cell / viral protein processing / receptor ligand activity / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / symbiont entry into host cell / virion attachment to host cell / host cell plasma membrane / virion membrane / structural molecule activity / membrane
Similarity search - Function
Envelope glycoprotein Gp160 / Retroviral envelope protein / Retroviral envelope protein GP41-like / Gp120 core superfamily / Envelope glycoprotein GP120 / Human immunodeficiency virus 1, envelope glycoprotein Gp120
Similarity search - Domain/homology
Envelope glycoprotein gp160 / Envelope glycoprotein gp160 / Env polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsXue, Y.
CitationJournal: To Be Published
Title: A new HIV fusion peptide inhibitor
Authors: Xue, Y.
History
DepositionMay 25, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 25, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: Envelope glycoprotein gp160
N: Envelope glycoprotein
A: Envelope glycoprotein gp160
B: Envelope glycoprotein
D: Envelope glycoprotein gp160
E: Envelope glycoprotein


Theoretical massNumber of molelcules
Total (without water)25,8306
Polymers25,8306
Non-polymers00
Water52229
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11400 Å2
ΔGint-94 kcal/mol
Surface area10600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.150, 52.340, 60.260
Angle α, β, γ (deg.)90.00, 117.46, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein/peptide Envelope glycoprotein gp160 / Endogenous retrovirus group K member 113 Env polyprotein / Endogenous retrovirus group K member 13- ...Endogenous retrovirus group K member 113 Env polyprotein / Endogenous retrovirus group K member 13-1 Env polyprotein / Endogenous retrovirus group K member 18 Env polyprotein / Endogenous retrovirus group K member 19 Env polyprotein / Endogenous retrovirus group K member 21 Env polyprotein / Endogenous retrovirus group K member 24 Env polyprotein / Endogenous retrovirus group K member 25 Env polyprotein / Endogenous retrovirus group K member 6 Env polyprotein / Endogenous retrovirus group K member 7 Env polyprotein / Endogenous retrovirus group K member 9 Env polyprotein / Envelope glycoprotein gp160


Mass: 4491.876 Da / Num. of mol.: 2 / Fragment: UNP residues 627-661 / Source method: obtained synthetically / Details: (ACE) is acetyl modification of the N terminal / Source: (synth.) Human immunodeficiency virus 1 / References: UniProt: B2CPZ5, UniProt: P04578*PLUS
#2: Protein/peptide Envelope glycoprotein


Mass: 4126.805 Da / Num. of mol.: 3 / Fragment: UNP residues 35-70 / Source method: obtained synthetically / Source: (synth.) Human immunodeficiency virus 1 / References: UniProt: Q1HMR5, UniProt: P04578*PLUS
#3: Protein/peptide Envelope glycoprotein gp160 / Endogenous retrovirus group K member 113 Env polyprotein / Endogenous retrovirus group K member 13- ...Endogenous retrovirus group K member 113 Env polyprotein / Endogenous retrovirus group K member 13-1 Env polyprotein / Endogenous retrovirus group K member 18 Env polyprotein / Endogenous retrovirus group K member 19 Env polyprotein / Endogenous retrovirus group K member 21 Env polyprotein / Endogenous retrovirus group K member 24 Env polyprotein / Endogenous retrovirus group K member 25 Env polyprotein / Endogenous retrovirus group K member 6 Env polyprotein / Endogenous retrovirus group K member 7 Env polyprotein / Endogenous retrovirus group K member 9 Env polyprotein / Envelope glycoprotein gp160


Mass: 4465.839 Da / Num. of mol.: 1 / Fragment: UNP residues 627-661 / Source method: obtained synthetically / Source: (synth.) Human immunodeficiency virus 1 / References: UniProt: B2CPZ5, UniProt: P04578*PLUS
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 29 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.09 Å3/Da / Density % sol: 41.14 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 0.1 M Calcium chloride 0.1 M Sodium acetate pH 4.6 15 %PEG 400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Jun 2, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.8→26.74 Å / Num. obs: 11921 / % possible obs: 92.3 % / Redundancy: 2.27 % / Net I/σ(I): 22.3

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Processing

Software
NameVersionClassification
PHENIX1.6.4_486refinement
d*TREKdata reduction
CrystalCleardata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→26.735 Å / SU ML: 0.49 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 27.61 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2883 247 4.95 %Random selection
Rwork0.2706 ---
obs0.2715 4994 93.17 %-
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 21.056 Å2 / ksol: 0.295 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--9.1434 Å2-0 Å20.6922 Å2
2---9.2057 Å20 Å2
3----12.8803 Å2
Refinement stepCycle: LAST / Resolution: 2.8→26.735 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1775 0 0 29 1804
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081796
X-RAY DIFFRACTIONf_angle_d1.1552425
X-RAY DIFFRACTIONf_dihedral_angle_d18.359677
X-RAY DIFFRACTIONf_chiral_restr0.074272
X-RAY DIFFRACTIONf_plane_restr0.003315
LS refinement shellResolution: 2.8→3.5265 Å
RfactorNum. reflection% reflection
Rfree0.2488 131 -
Rwork0.2411 2397 -
obs--95 %

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