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- PDB-2r5d: Structure of the gp41 N-trimer in complex with the HIV entry inhi... -

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Basic information

Entry
Database: PDB / ID: 2r5d
TitleStructure of the gp41 N-trimer in complex with the HIV entry inhibitor PIE7
Components
  • HIV entry inhibitor PIE7
  • gp41 N-peptide
KeywordsVIRAL PROTEIN/inhibitor / HIV / viral entry / PIE / 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 PIE7 / polypeptide(D) / polypeptide(D) (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / Resolution: 1.66 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
DepositionSep 3, 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 1.2Dec 12, 2012Group: Other
Revision 1.3Oct 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 1.4Oct 30, 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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: gp41 N-peptide
H: HIV entry inhibitor PIE7
K: HIV entry inhibitor PIE7
L: HIV entry inhibitor PIE7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,1219
Polymers21,6956
Non-polymers4263
Water3,351186
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10440 Å2
ΔGint-101 kcal/mol
Surface area10990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.438, 56.345, 53.424
Angle α, β, γ (deg.)90.000, 96.900, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein/peptide / Polypeptide(D) , 2 types, 6 molecules ABCHKL

#1: Protein/peptide gp41 N-peptide


Mass: 5466.574 Da / Num. of mol.: 3 / Source method: obtained synthetically / Details: peptide synthesis / Source: (synth.) synthetic construct (others)
#2: Polypeptide(D) HIV entry inhibitor PIE7


Type: Peptide-like / Class: Inhibitor / Mass: 1765.001 Da / Num. of mol.: 3 / Source method: obtained synthetically / Details: peptide synthesis / Source: (synth.) synthetic construct (others) / References: HIV ENTRY INHIBITOR PIE7

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Non-polymers , 4 types, 189 molecules

#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 186 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.46 Å3/Da / Density % sol: 49.94 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 7.5
Details: 0.1M HEPES, 24% PEG 10000, pH 7.5, vapor diffusion, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.541 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Apr 4, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.541 Å / Relative weight: 1
ReflectionResolution: 1.66→50 Å / Num. all: 24829 / Num. obs: 23406 / % possible obs: 94.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.3 % / Rmerge(I) obs: 0.046 / Χ2: 1.625 / Net I/σ(I): 21.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.66-1.721.70.31515201.154162.1
1.72-1.791.90.3321031.192185.3
1.79-1.872.30.34924551.332199.2
1.87-1.972.40.25124841.654199.6
1.97-2.092.40.15524621.871199.7
2.09-2.252.40.1124442.154199.6
2.25-2.482.40.08224732.025199.9
2.48-2.842.50.06324871.612199.9
2.84-3.582.50.04624941.409199.6
3.58-502.50.03124841.338197.5

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3data extraction
CrystalCleardata collection
PHASERphasing
RefinementResolution: 1.66→38.63 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.944 / SU B: 5.434 / SU ML: 0.092 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.171 / ESU R Free: 0.122 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.249 1195 5.1 %RANDOM
Rwork0.201 ---
obs0.204 23228 93.73 %-
all-25953 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.427 Å2
Baniso -1Baniso -2Baniso -3
1--0.18 Å20 Å20.6 Å2
2--0.89 Å20 Å2
3----0.57 Å2
Refinement stepCycle: LAST / Resolution: 1.66→38.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1527 0 26 186 1739
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0221600
X-RAY DIFFRACTIONr_angle_refined_deg1.162.0012139
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.7655180
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.14425.96252
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.25315298
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.973159
X-RAY DIFFRACTIONr_chiral_restr0.0660.2226
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021115
X-RAY DIFFRACTIONr_nbd_refined0.2030.2845
X-RAY DIFFRACTIONr_nbtor_refined0.2930.21107
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1130.2127
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.220.248
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.140.212
X-RAY DIFFRACTIONr_mcbond_it1.4161.5977
X-RAY DIFFRACTIONr_mcangle_it2.15321498
X-RAY DIFFRACTIONr_scbond_it3.4793742
X-RAY DIFFRACTIONr_scangle_it5.1994.5641
LS refinement shellResolution: 1.66→1.703 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.442 56 -
Rwork0.299 1038 -
all-1094 -
obs--59.68 %

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