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- PDB-6tvw: Structure of native gp41 derived peptide fusion inhibitor -

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Basic information

Entry
Database: PDB / ID: 6tvw
TitleStructure of native gp41 derived peptide fusion inhibitor
Components
  • ASN-ASN-TYR-THR-SER-LEU-ILE-HIS-SER-LEU-ILE-GLU-GLU
  • Envelope glycoprotein
  • MET-THR-TRP-MET-GLU-TRP-ASP-ARG-GLU
KeywordsVIRAL PROTEIN / Inhibitor / helix bundle / HIV
Function / homologyRetroviral envelope protein / Retroviral envelope protein GP41-like / viral envelope / host cell plasma membrane / virion membrane / structural molecule activity / plasma membrane / Chem-O0B / Env polyprotein
Function and homology information
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 1.45 Å
AuthorsHuhmann, S. / Nyakatura, E.K. / Rohrhofer, A. / Schmidt, B. / Eichler, J. / Moschner, J. / Roth, C. / Koksch, B.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG) Germany
CitationJournal: Chembiochem / Year: 2021
Title: Systematic Evaluation of Fluorination as Modification for Peptide-Based Fusion Inhibitors against HIV-1 Infection.
Authors: Huhmann, S. / Nyakatura, E.K. / Rohrhofer, A. / Moschner, J. / Schmidt, B. / Eichler, J. / Roth, C. / Koksch, B.
History
DepositionJan 10, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 27, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 16, 2022Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.0Nov 15, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / atom_type / chem_comp_atom / chem_comp_bond / pdbx_validate_close_contact / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _pdbx_validate_close_contact.auth_atom_id_2 / _struct_conn.ptnr2_label_atom_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
CCC: Envelope glycoprotein
DDD: MET-THR-TRP-MET-GLU-TRP-ASP-ARG-GLU
DbD: ASN-ASN-TYR-THR-SER-LEU-ILE-HIS-SER-LEU-ILE-GLU-GLU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,4794
Polymers8,3093
Non-polymers1691
Water1,33374
1
CCC: Envelope glycoprotein
DDD: MET-THR-TRP-MET-GLU-TRP-ASP-ARG-GLU
DbD: ASN-ASN-TYR-THR-SER-LEU-ILE-HIS-SER-LEU-ILE-GLU-GLU
hetero molecules

CCC: Envelope glycoprotein
DDD: MET-THR-TRP-MET-GLU-TRP-ASP-ARG-GLU
DbD: ASN-ASN-TYR-THR-SER-LEU-ILE-HIS-SER-LEU-ILE-GLU-GLU
hetero molecules

CCC: Envelope glycoprotein
DDD: MET-THR-TRP-MET-GLU-TRP-ASP-ARG-GLU
DbD: ASN-ASN-TYR-THR-SER-LEU-ILE-HIS-SER-LEU-ILE-GLU-GLU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,43612
Polymers24,9289
Non-polymers5073
Water1629
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-y-1,x-y,z1
crystal symmetry operation3_445-x+y-1,-x-1,z1
Unit cell
Length a, b, c (Å)44.706, 44.706, 208.857
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11CCC-622-

HOH

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Components

#1: Protein/peptide Envelope glycoprotein


Mass: 4491.245 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Human immunodeficiency virus 1 / References: UniProt: Q5VGF0
#2: Protein/peptide MET-THR-TRP-MET-GLU-TRP-ASP-ARG-GLU


Mass: 2069.255 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Human immunodeficiency virus 1
#3: Protein/peptide ASN-ASN-TYR-THR-SER-LEU-ILE-HIS-SER-LEU-ILE-GLU-GLU


Mass: 1748.866 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Human immunodeficiency virus 1
#4: Chemical ChemComp-O0B / (2~{S},3~{S})-2-azanyl-5,5,5-tris(fluoranyl)-3-methyl-pentanal


Mass: 169.145 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H10F3NO / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 74 / 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: 2.42 Å3/Da / Density % sol: 49.11 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion / Details: PEG 3350, ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 6, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.45→69.7 Å / Num. obs: 14813 / % possible obs: 99.9 % / Redundancy: 13.5 % / CC1/2: 0.997 / Rpim(I) all: 0.048 / Net I/σ(I): 6.5
Reflection shellResolution: 1.45→1.47 Å / Mean I/σ(I) obs: 1.2 / Num. unique obs: 713 / CC1/2: 0.887

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
Aimlessdata scaling
ACORNphasing
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 1.45→69.619 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.923 / SU B: 9.118 / SU ML: 0.135 / Cross valid method: FREE R-VALUE / ESU R: 0.093 / ESU R Free: 0.092
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2983 690 4.658 %
Rwork0.2338 --
all0.237 --
obs-14813 99.852 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 32.952 Å2
Baniso -1Baniso -2Baniso -3
1-3.672 Å21.836 Å20 Å2
2--3.672 Å20 Å2
3----11.911 Å2
Refinement stepCycle: LAST / Resolution: 1.45→69.619 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms512 0 11 74 597
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.013556
X-RAY DIFFRACTIONr_bond_other_d0.0020.017521
X-RAY DIFFRACTIONr_angle_refined_deg1.5011.631754
X-RAY DIFFRACTIONr_angle_other_deg1.451.5891208
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.632563
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.19721.15426
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.361593
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.302154
X-RAY DIFFRACTIONr_chiral_restr0.0750.273
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02607
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02113
X-RAY DIFFRACTIONr_nbd_refined0.3080.2164
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2410.2457
X-RAY DIFFRACTIONr_nbtor_refined0.1690.2265
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0920.2223
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2080.241
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.090.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1990.224
X-RAY DIFFRACTIONr_nbd_other0.2220.279
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1870.28
X-RAY DIFFRACTIONr_mcbond_it3.7052.965252
X-RAY DIFFRACTIONr_mcbond_other3.7022.982253
X-RAY DIFFRACTIONr_mcangle_it4.7084.462315
X-RAY DIFFRACTIONr_mcangle_other4.7014.481316
X-RAY DIFFRACTIONr_scbond_it7.683.713304
X-RAY DIFFRACTIONr_scbond_other7.693.702303
X-RAY DIFFRACTIONr_scangle_it7.3235.365439
X-RAY DIFFRACTIONr_scangle_other7.3155.378440
X-RAY DIFFRACTIONr_lrange_it6.60339.169705
X-RAY DIFFRACTIONr_lrange_other6.3338.475689
X-RAY DIFFRACTIONr_rigid_bond_restr7.60531073
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.45-1.4880.758620.5591022X-RAY DIFFRACTION100
1.488-1.5280.434400.443984X-RAY DIFFRACTION100
1.528-1.5730.615460.393985X-RAY DIFFRACTION99.9031
1.573-1.6210.484520.36927X-RAY DIFFRACTION99.898
1.621-1.6740.318480.343913X-RAY DIFFRACTION99.896
1.674-1.7330.364430.303903X-RAY DIFFRACTION100
1.733-1.7980.283400.253854X-RAY DIFFRACTION100
1.798-1.8720.372380.245836X-RAY DIFFRACTION100
1.872-1.9550.26440.236789X-RAY DIFFRACTION100
1.955-2.050.225290.211769X-RAY DIFFRACTION99.8748
2.05-2.1610.257290.187742X-RAY DIFFRACTION100
2.161-2.2920.201230.177693X-RAY DIFFRACTION99.8605
2.292-2.450.259300.188665X-RAY DIFFRACTION100
2.45-2.6460.228350.203608X-RAY DIFFRACTION99.8447
2.646-2.8980.198340.184550X-RAY DIFFRACTION100
2.898-3.2390.384240.206521X-RAY DIFFRACTION99.4526
3.239-3.7390.235310.199451X-RAY DIFFRACTION99.3814
3.739-4.5760.315170.173392X-RAY DIFFRACTION98.7923
4.576-6.4580.201150.227323X-RAY DIFFRACTION99.4118
6.458-69.60.347100.265195X-RAY DIFFRACTION99.5146

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