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- PDB-3l37: PIE12 D-peptide against HIV entry -

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Basic information

Entry
Database: PDB / ID: 3l37
TitlePIE12 D-peptide against HIV entry
Components
  • GP41 N-PEPTIDE
  • HIV ENTRY INHIBITOR PIE12
KeywordsDE NOVO PROTEIN / COILED-COIL / D-PEPTIDE INHIBITOR
Function / homologySingle alpha-helices involved in coiled-coils or other helix-helix interfaces - #170 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Mainly Alpha
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsWelch, B.D. / Redman, J.S. / Paul, S. / Whitby, F.G. / Weinstock, M.T. / Reeves, J.D. / Lie, Y.S. / Eckert, D.M. / Hill, C.P. / Root, M.J. / Kay, M.S.
CitationJournal: J.Virol. / Year: 2010
Title: Design of a potent D-peptide HIV-1 entry inhibitor with a strong barrier to resistance.
Authors: Welch, B.D. / Francis, J.N. / Redman, J.S. / Paul, S. / Weinstock, M.T. / Reeves, J.D. / Lie, Y.S. / Whitby, F.G. / Eckert, D.M. / Hill, C.P. / Root, M.J. / Kay, M.S.
History
DepositionDec 16, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 3, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GP41 N-PEPTIDE
H: HIV ENTRY INHIBITOR PIE12


Theoretical massNumber of molelcules
Total (without water)7,4962
Polymers7,4962
Non-polymers00
Water64936
1
A: GP41 N-PEPTIDE
H: HIV ENTRY INHIBITOR PIE12

A: GP41 N-PEPTIDE
H: HIV ENTRY INHIBITOR PIE12

A: GP41 N-PEPTIDE
H: HIV ENTRY INHIBITOR PIE12


Theoretical massNumber of molelcules
Total (without water)22,4886
Polymers22,4886
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-y,x-y+1,z1
crystal symmetry operation3_455-x+y-1,-x,z1
Buried area10670 Å2
ΔGint-86 kcal/mol
Surface area11170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.121, 49.121, 67.687
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11A-47-

HOH

DetailsBIOMOLECULE: 1, 2, 3 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON BURIED SURFACE AREA. COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. BIOMOLECULE: 1 AUTHOR DETERMINED BIOLOGICAL UNIT: HEXAMERIC SOFTWARE DETERMINED QUATERNARY STRUCTURE: HEXAMERIC SOFTWARE USED: PISA TOTAL BURIED SURFACE AREA: 10690 ANGSTROM**2 SURFACE AREA OF THE COMPLEX: 11170 ANGSTROM**2 CHANGE IN SOLVENT FREE ENERGY: -86.0 KCAL/MOL APPLY THE FOLLOWING TO CHAINS: A, H BIOMT1 1 1.000000 0.000000 0.000000 0.00000 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 BIOMT1 2 -0.500000 -0.866025 0.000000 -24.56050 BIOMT2 2 0.866025 -0.500000 0.000000 42.54003 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 BIOMT1 3 -0.500000 0.866025 0.000000 -49.12100 BIOMT2 3 -0.866025 -0.500000 0.000000 0.00000 BIOMT3 3 0.000000 0.000000 1.000000 0.00000 BIOMOLECULE: 2 AUTHOR DETERMINED BIOLOGICAL UNIT: HEXAMERIC SOFTWARE DETERMINED QUATERNARY STRUCTURE: HEXAMERIC SOFTWARE USED: PISA TOTAL BURIED SURFACE AREA: 8000 ANGSTROM**2 SURFACE AREA OF THE COMPLEX: 13850 ANGSTROM**2 CHANGE IN SOLVENT FREE ENERGY: -47.0 KCAL/MOL APPLY THE FOLLOWING TO CHAINS: A BIOMT1 1 1.000000 0.000000 0.000000 0.00000 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 BIOMT1 2 -0.500000 -0.866025 0.000000 -24.56050 BIOMT2 2 0.866025 -0.500000 0.000000 42.54003 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 BIOMT1 3 -0.500000 0.866025 0.000000 -49.12100 BIOMT2 3 -0.866025 -0.500000 0.000000 0.00000 BIOMT3 3 0.000000 0.000000 1.000000 0.00000 APPLY THE FOLLOWING TO CHAINS: H BIOMT1 4 1.000000 0.000000 0.000000 -24.56050 BIOMT2 4 0.000000 1.000000 0.000000 -14.18001 BIOMT3 4 0.000000 0.000000 1.000000 45.12467 BIOMT1 5 -0.500000 -0.866025 0.000000 0.00000 BIOMT2 5 0.866025 -0.500000 0.000000 28.36002 BIOMT3 5 0.000000 0.000000 1.000000 45.12467 BIOMT1 6 -0.500000 0.866025 0.000000 -49.12100 BIOMT2 6 -0.866025 -0.500000 0.000000 28.36002 BIOMT3 6 0.000000 0.000000 1.000000 45.12467 BIOMOLECULE: 3 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC SOFTWARE USED: PISA TOTAL BURIED SURFACE AREA: 1410 ANGSTROM**2 SURFACE AREA OF THE COMPLEX: 5880 ANGSTROM**2 CHANGE IN SOLVENT FREE ENERGY: -7.0 KCAL/MOL APPLY THE FOLLOWING TO CHAINS: A, H BIOMT1 1 1.000000 0.000000 0.000000 0.00000 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 BIOMT3 1 0.000000 0.000000 1.000000 0.00000

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Components

#1: Protein/peptide GP41 N-PEPTIDE


Mass: 5466.574 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: L-PEPTIDE WITH N-TERMINAL ACETYL GROUP AND C-TERMINAL AMIDE GROUP
#2: Protein/peptide HIV ENTRY INHIBITOR PIE12


Mass: 2029.301 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: D-PEPTIDE WITH N-TERMINAL ACETYL GROUP AND C-TERMINAL AMIDE GROUP
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 36 / 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: 2.1 Å3/Da / Density % sol: 41.33 %
Crystal growpH: 8
Details: 100 MM IMIDIZOLE, PH 8.0, 50% (V/V) ETHYLENE GLYCOL, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.97945
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jun 8, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97945 Å / Relative weight: 1
ReflectionResolution: 1.45→30 Å / Num. obs: 10475 / % possible obs: 97.1 % / Observed criterion σ(I): 0 / Redundancy: 9.4 % / Rmerge(I) obs: 0.058 / Net I/σ(I): 28.289
Reflection shellResolution: 1.45→1.5 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.102 / % possible all: 80.1

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Processing

Software
NameVersionClassification
PHASERphasing
REFMAC5.5.0062refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.45→24.56 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.937 / SU B: 1.664 / SU ML: 0.065 / Cross valid method: THROUGHOUT / ESU R: 0.1 / ESU R Free: 0.098 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.264 1026 9.8 %RANDOM
Rwork0.235 ---
obs0.238 9448 97.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.93 Å2
Baniso -1Baniso -2Baniso -3
1-1.27 Å20.64 Å20 Å2
2--1.27 Å20 Å2
3----1.91 Å2
Refinement stepCycle: LAST / Resolution: 1.45→24.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms528 0 0 36 564
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.022538
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6932.11704
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.937556
X-RAY DIFFRACTIONr_dihedral_angle_2_deg47.91525.88217
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.7011598
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.539153
X-RAY DIFFRACTIONr_chiral_restr0.0870.276
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021359
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0051.5311
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.9542489
X-RAY DIFFRACTIONr_scbond_it2.8023226
X-RAY DIFFRACTIONr_scangle_it4.7034.5215
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.45→1.49 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.392 63 -
Rwork0.301 541 -
obs--77.63 %

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