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- PDB-2r3c: Structure of the gp41 N-peptide in complex with the HIV entry inh... -

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Basic information

Entry
Database: PDB / ID: 2r3c
TitleStructure of the gp41 N-peptide in complex with the HIV entry inhibitor PIE1
Components
  • HIV entry inhibitor PIE1
  • gp41 N-peptide
KeywordsVIRAL PROTEIN/VIRAL PROTEIN INHIBITOR / HIV / inhibitor / viral entry / PIE / VIRAL PROTEIN / VIRAL PROTEIN-VIRAL PROTEIN INHIBITOR complex
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 / HIV entry inhibitor PIE1 / YTTRIUM (III) ION / polypeptide(D) / polypeptide(D) (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.73 Å
AuthorsVanDemark, A.P. / Welch, B. / Heroux, A. / Hill, C.P. / Kay, M.S.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2007
Title: Potent D-peptide inhibitors of HIV-1 entry
Authors: Welch, B.D. / Vandemark, A.P. / Heroux, A. / Hill, C.P. / Kay, M.S.
History
DepositionAug 29, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 2, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Structure summary / Version format compliance
Revision 1.2Feb 15, 2012Group: Structure summary
Revision 1.3Dec 12, 2012Group: Other
Revision 1.4Oct 25, 2017Group: Refinement description / Source and taxonomy / Category: pdbx_entity_src_syn / software
Item: _pdbx_entity_src_syn.ncbi_taxonomy_id / _pdbx_entity_src_syn.organism_scientific
Revision 1.5Aug 8, 2018Group: Data collection / Database references / Derived calculations
Category: pdbx_struct_conn_angle / struct_conn / struct_ref_seq
Item: _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: gp41 N-peptide
B: gp41 N-peptide
C: HIV entry inhibitor PIE1
D: HIV entry inhibitor PIE1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,07510
Polymers14,5954
Non-polymers4806
Water3,783210
1
A: gp41 N-peptide
D: HIV entry inhibitor PIE1
hetero molecules

A: gp41 N-peptide
D: HIV entry inhibitor PIE1
hetero molecules

A: gp41 N-peptide
D: HIV entry inhibitor PIE1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,53315
Polymers21,8936
Non-polymers6409
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area10020 Å2
ΔGint-88 kcal/mol
Surface area11230 Å2
MethodPISA
2
B: gp41 N-peptide
C: HIV entry inhibitor PIE1
hetero molecules

B: gp41 N-peptide
C: HIV entry inhibitor PIE1
hetero molecules

B: gp41 N-peptide
C: HIV entry inhibitor PIE1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,69315
Polymers21,8936
Non-polymers8009
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area9400 Å2
ΔGint-103 kcal/mol
Surface area9790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.843, 46.843, 137.079
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63
Components on special symmetry positions
IDModelComponents
11A-502-

YT3

21A-503-

CL

31B-102-

YT3

41B-103-

YT3

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Components

#1: Protein/peptide gp41 N-peptide


Mass: 5466.574 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: peptide synthesis / Source: (synth.) synthetic construct (others)
#2: Polypeptide(D) HIV entry inhibitor PIE1


Type: Peptide-like / Class: Inhibitor / Mass: 1831.103 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: peptide synthesis / Source: (synth.) synthetic construct (others) / References: HIV entry inhibitor PIE1
#3: Chemical
ChemComp-YT3 / YTTRIUM (III) ION / Yttrium


Mass: 88.906 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Y
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 210 / 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: 2.99 Å3/Da / Density % sol: 58.92 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 4.6
Details: 27% PEG 2000 MME, 0.1M Sodium Acetate, 0.4M YCl3, pH 4.6, VAPOR DIFFUSION, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X26C / Wavelength: 1.07274 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 8, 2004
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07274 Å / Relative weight: 1
Reflection twinType: hemihedral / Operator: h,-h-k,-l / Fraction: 0.326
ReflectionResolution: 1.73→50 Å / Num. all: 35168 / Num. obs: 33506 / % possible obs: 95.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.6 % / Rmerge(I) obs: 0.094 / Χ2: 1.327 / Net I/σ(I): 14.5
Reflection shellResolution: 1.73→1.79 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.481 / Num. unique all: 2716 / Χ2: 0.864 / % possible all: 77.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
CNSrefinement
PDB_EXTRACT3data extraction
ADSCQuantumdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.73→50 Å / Isotropic thermal model: isotropic / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: Data has a twin fraction of 0.326
RfactorNum. reflection% reflectionSelection details
Rfree0.23 1510 4.3 %selected randomly with equal numbers in each resolution bin. Total number of reflections to exceed 1500.
Rwork0.193 ---
all0.23 35155 --
obs0.23 32413 92.2 %-
Solvent computationBsol: 53.063 Å2
Displacement parametersBiso mean: 30.006 Å2
Baniso -1Baniso -2Baniso -3
1--5.192 Å2-3.309 Å20 Å2
2---5.192 Å20 Å2
3---10.385 Å2
Refinement stepCycle: LAST / Resolution: 1.73→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms962 0 6 210 1178
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it1.1071.5
X-RAY DIFFRACTIONc_scbond_it2.3412
X-RAY DIFFRACTIONc_mcangle_it1.7822
X-RAY DIFFRACTIONc_scangle_it3.6762.5
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_wcaps.param
X-RAY DIFFRACTION2water_rep.param
X-RAY DIFFRACTION3ion.param

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