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- PDB-3l35: PIE12 D-peptide against HIV entry -

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Basic information

Entry
Database: PDB / ID: 3l35
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 / MOLECULAR REPLACEMENT / Resolution: 1.55 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
Revision 1.2Nov 20, 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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GP41 N-PEPTIDE
B: GP41 N-PEPTIDE
C: GP41 N-PEPTIDE
H: HIV ENTRY INHIBITOR PIE12
K: HIV ENTRY INHIBITOR PIE12
L: HIV ENTRY INHIBITOR PIE12


Theoretical massNumber of molelcules
Total (without water)22,4886
Polymers22,4886
Non-polymers00
Water3,549197
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10570 Å2
ΔGint-84 kcal/mol
Surface area10620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)30.850, 40.487, 80.306
Angle α, β, γ (deg.)90.00, 91.76, 90.00
Int Tables number4
Space group name H-MP1211
DetailsBIOMOLECULE: 1 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: 10560 ANGSTROM**2 SURFACE AREA OF THE COMPLEX: 10620 ANGSTROM**2 CHANGE IN SOLVENT FREE ENERGY: -84.0 KCAL/MOL APPLY THE FOLLOWING TO CHAINS: A, B, C, H, K, L 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.: 3 / 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.: 3 / Source method: obtained synthetically
Details: D-PEPTIDE WITH N-TERMINAL ACETYL GROUP AND C-TERMINAL AMIDE GROUP
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 197 / 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 / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.23 Å3/Da / Density % sol: 44.82 %
Crystal growpH: 9
Details: 0.1 M BICINE, 2% V/V 1,4-DIOXANE, 10% W/V POLYETHYLENE GLYCOL 20,000, PH 9.0, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jun 11, 2008 / Details: VARIMAX-HR
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.55→30 Å / Num. obs: 25088 / % possible obs: 86.5 % / Observed criterion σ(I): 0 / Redundancy: 4.5 % / Rmerge(I) obs: 0.051 / Net I/σ(I): 21.669
Reflection shellResolution: 1.55→1.61 Å / Redundancy: 3 % / Rmerge(I) obs: 0.25 / % possible all: 66.8

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Processing

Software
NameVersionClassification
PHASERphasing
REFMAC5.5.0062refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.55→30 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.917 / SU B: 2.053 / SU ML: 0.076 / Cross valid method: THROUGHOUT / ESU R: 0.126 / ESU R Free: 0.131 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.288 1273 5.1 %RANDOM
Rwork0.233 ---
obs0.235 23765 86.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.98 Å2
Baniso -1Baniso -2Baniso -3
1-0.38 Å20 Å21.11 Å2
2--0.51 Å20 Å2
3----0.82 Å2
Refinement stepCycle: LAST / Resolution: 1.55→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1572 0 0 197 1769
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0221630
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.442.1032129
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.385171
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.68125.6653
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.56815299
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.8361510
X-RAY DIFFRACTIONr_chiral_restr0.0790.2229
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211098
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_it0.8031.5937
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.53721477
X-RAY DIFFRACTIONr_scbond_it2.7133684
X-RAY DIFFRACTIONr_scangle_it4.4514.5652
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.55→1.59 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.623 78 -
Rwork0.465 1224 -
obs--62.72 %

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