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- PDB-5y14: Crystal structure of LP-40/N44 -

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Basic information

Entry
Database: PDB / ID: 5y14
TitleCrystal structure of LP-40/N44
Components
  • LP-40
  • N44
KeywordsVIRAL PROTEIN/INHIBITOR / 6-HB / HIV-1 / VIRAL PROTEIN-INHIBITOR complex
Function / homologyRetroviral envelope protein / Retroviral envelope protein GP41-like / viral envelope / host cell plasma membrane / virion membrane / structural molecule activity / plasma membrane / Env polyprotein
Function and homology information
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.762 Å
AuthorsZhang, X. / Wang, X. / He, Y.
Funding support China, 1items
OrganizationGrant numberCountry
Natural Science Foundation of China81630061, 81473255, 81673484, and 81271830 China
CitationJournal: J. Virol. / Year: 2017
Title: Enfuvirtide (T20)-Based Lipopeptide Is a Potent HIV-1 Cell Fusion Inhibitor: Implications for Viral Entry and Inhibition
Authors: Ding, X. / Zhang, X. / Chong, H. / Zhu, Y. / Wei, H. / Wu, X. / He, J. / Wang, X. / He, Y.
History
DepositionJul 19, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 8, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: N44
B: N44
A: N44
F: LP-40
E: LP-40
D: LP-40


Theoretical massNumber of molelcules
Total (without water)25,2026
Polymers25,2026
Non-polymers00
Water2,378132
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11000 Å2
ΔGint-91 kcal/mol
Surface area10850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.830, 36.140, 53.440
Angle α, β, γ (deg.)90.00, 99.87, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein/peptide N44


Mass: 5037.884 Da / Num. of mol.: 3 / Fragment: UNP residues 27-70 / Source method: obtained synthetically / Source: (synth.) Human immunodeficiency virus 1 / References: UniProt: Q1HMR5
#2: Protein/peptide LP-40


Mass: 3362.629 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) Human immunodeficiency virus 1
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 132 / Source method: isolated from a natural source / Formula: H2O

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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: 1.92 Å3/Da / Density % sol: 35.9 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / Details: 2.2M Sodium chloride, 0.1M Tris pH 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9796 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 27, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 1.76→50 Å / Num. obs: 17147 / % possible obs: 90.4 % / Redundancy: 3.8 % / Net I/σ(I): 16

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Processing

Software
NameVersionClassification
HKL-2000(1.10.1_2155: ???)data processing
Cootmodel building
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.762→24.284 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 26.04
RfactorNum. reflection% reflection
Rfree0.2506 935 5.46 %
Rwork0.2074 --
obs0.2099 17132 89.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.762→24.284 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1720 0 0 132 1852
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061728
X-RAY DIFFRACTIONf_angle_d0.6622329
X-RAY DIFFRACTIONf_dihedral_angle_d11.9161075
X-RAY DIFFRACTIONf_chiral_restr0.039283
X-RAY DIFFRACTIONf_plane_restr0.004302
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7621-1.8550.27661490.21192283X-RAY DIFFRACTION90
1.855-1.97110.27091320.20182336X-RAY DIFFRACTION91
1.9711-2.12320.25021360.19722363X-RAY DIFFRACTION91
2.1232-2.33670.22571420.17512329X-RAY DIFFRACTION91
2.3367-2.67450.25191130.18062367X-RAY DIFFRACTION90
2.6745-3.36820.24141310.21582351X-RAY DIFFRACTION90
3.3682-24.28620.25771320.22812168X-RAY DIFFRACTION82
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.35780.02220.17780.93451.01912.1981-0.1953-0.17610.04070.4427-0.05770.16960.5886-0.2136-0.01610.1309-0.00050.04280.207-0.09250.17977.23060.028822.7923
2-0.08860.2726-0.04550.69780.18861.692-0.0245-0.06590.05980.00060.1137-0.0250.04580.4224-0.06940.10040.0301-0.01730.192-0.06870.126314.38014.633621.0062
31.3149-0.3055-0.34451.4835-0.32342.948-0.0252-0.1140.0824-0.702-0.27530.2426-1.1983-0.6524-0.05310.06680.0277-0.00560.1242-0.04380.15486.60897.96917.9301
41.9078-0.40310.47671.42380.36772.0440.0540.08630.31050.2416-0.55590.51770.2721-1.0287-0.08310.1876-0.02530.02310.2226-0.06890.29640.4097-4.706412.212
51.33420.16710.29191.6924-0.08951.4275-0.3724-0.1153-0.31420.33450.0051-0.07930.82730.1939-0.07360.22070.0365-0.02770.17480.01390.157118.6115-6.5216.7344
61.72790.234-0.19652.27031.68253.49640.02980.01250.4714-0.57980.0306-0.0545-0.84980.34160.06220.3174-0.0013-0.01060.1568-0.01860.327612.3638.36265.3279
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'S' and (resid 28 through 71 )
2X-RAY DIFFRACTION2chain 'B' and (resid 27 through 70 )
3X-RAY DIFFRACTION3chain 'A' and (resid 27 through 70 )
4X-RAY DIFFRACTION4chain 'W' and (resid 127 through 153 )
5X-RAY DIFFRACTION5chain 'Q' and (resid 127 through 152 )
6X-RAY DIFFRACTION6chain 'P' and (resid 127 through 152 )

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