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- PDB-1czq: CRYSTAL STRUCTURE OF THE D10-P1/IQN17 COMPLEX: A D-PEPTIDE INHIBI... -

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Basic information

Entry
Database: PDB / ID: 1czq
TitleCRYSTAL STRUCTURE OF THE D10-P1/IQN17 COMPLEX: A D-PEPTIDE INHIBITOR OF HIV-1 ENTRY BOUND TO THE GP41 COILED-COIL POCKET.
Components
  • D-PEPTIDE INHIBITOR
  • FUSION PROTEIN BETWEEN THE HYDROPHOBIC POCKET OF HIV GP41 AND GCN4-PIQI
KeywordsViral protein/inhibitor / ENVELOPE GLYCOPROTEIN / 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 / :
Function and homology information
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Human immunodeficiency virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.5 Å
AuthorsEckert, D.M. / Malashkevich, V.N. / Hong, L.H. / Carr, P.A. / Kim, P.S.
Citation
Journal: Cell(Cambridge,Mass.) / Year: 1999
Title: Inhibiting HIV-1 entry: discovery of D-peptide inhibitors that target the gp41 coiled-coil pocket.
Authors: Eckert, D.M. / Malashkevich, V.N. / Hong, L.H. / Carr, P.A. / Kim, P.S.
#1: Journal: J.Mol.Biol. / Year: 1998
Title: Crystal structure of GCN4-pIQI, a trimeric coiled-coil with buried polar residues.
#2: Journal: Cell(Cambridge,Mass.) / Year: 1997
Title: Core structure of gp41 from the HIV envelope glycoprotein
History
DepositionSep 6, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 13, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Structure summary / Version format compliance
Revision 1.3Nov 13, 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_leaving_atom_flag / _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

Downloads & links

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Assembly

Deposited unit
A: FUSION PROTEIN BETWEEN THE HYDROPHOBIC POCKET OF HIV GP41 AND GCN4-PIQI
D: D-PEPTIDE INHIBITOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,3633
Polymers7,3282
Non-polymers351
Water2,702150
1
A: FUSION PROTEIN BETWEEN THE HYDROPHOBIC POCKET OF HIV GP41 AND GCN4-PIQI
D: D-PEPTIDE INHIBITOR
hetero molecules

A: FUSION PROTEIN BETWEEN THE HYDROPHOBIC POCKET OF HIV GP41 AND GCN4-PIQI
D: D-PEPTIDE INHIBITOR
hetero molecules

A: FUSION PROTEIN BETWEEN THE HYDROPHOBIC POCKET OF HIV GP41 AND GCN4-PIQI
D: D-PEPTIDE INHIBITOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,0899
Polymers21,9836
Non-polymers1063
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 area9460 Å2
ΔGint-115 kcal/mol
Surface area10980 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)41.829, 41.829, 84.817
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number150
Space group name H-MP321
Components on special symmetry positions
IDModelComponents
11A-1001-

CL

21A-1020-

HOH

31A-1063-

HOH

41A-1088-

HOH

51A-1107-

HOH

61A-1109-

HOH

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Components

#1: Protein/peptide FUSION PROTEIN BETWEEN THE HYDROPHOBIC POCKET OF HIV GP41 AND GCN4-PIQI / IQN17


Mass: 5468.566 Da / Num. of mol.: 1 / Fragment: HYDROPHOBIC POCKET
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae, Human immunodeficiency virus
Genus: Saccharomyces, Lentivirus / Species: , / Strain: , / References: GenBank: 1587615
#2: Protein/peptide D-PEPTIDE INHIBITOR / D10-P1


Mass: 1859.119 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: THIS PEPTIDE WAS CHEMICALLY SYNTHESIZED
#3: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 150 / 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: 2.7 Å3/Da / Density % sol: 53.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 10% PEG 4000 0.1 M SODIUM CITRATE 20% 2-PROPANOL, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal
*PLUS
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
11.4 mMIQN171drop
21.5 mMD10-p11drop
310 %PEG40001reservoir
40.1 Msodium citrate1reservoir
520 %2-propanol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 1.1197, 1.1393, 1.1403, 1.1399
DetectorType: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Mar 24, 1999
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.11971
21.13931
31.14031
41.13991
ReflectionResolution: 1.5→35 Å / Num. all: 14503 / Num. obs: 13604 / % possible obs: 93.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.5 % / Biso Wilson estimate: 21.6 Å2 / Rmerge(I) obs: 0.048 / Net I/σ(I): 16.8
Reflection shellResolution: 1.5→1.55 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.235 / Mean I/σ(I) obs: 4.5 / % possible all: 86.8

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
MLPHAREphasing
CNS0.5refinement
RefinementResolution: 1.5→10 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 646169.44 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.245 1362 10 %RANDOM
Rwork0.214 ---
all0.214 14322 --
obs0.214 13549 94.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 58.34 Å2 / ksol: 0.394 e/Å3
Displacement parametersBiso mean: 29.7 Å2
Baniso -1Baniso -2Baniso -3
1-3.61 Å21.74 Å20 Å2
2--3.61 Å20 Å2
3----7.22 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.2 Å0.18 Å
Luzzati d res low-5 Å
Luzzati sigma a0.12 Å0.09 Å
Refinement stepCycle: LAST / Resolution: 1.5→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms515 0 1 150 666
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.012
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d15.7
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it0.9562
X-RAY DIFFRACTIONc_mcangle_it1.5033
X-RAY DIFFRACTIONc_scbond_it1.8533
X-RAY DIFFRACTIONc_scangle_it2.6763.5
LS refinement shellResolution: 1.5→1.59 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.27 219 9.8 %
Rwork0.233 2008 -
obs--96.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP_D.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
Software
*PLUS
Name: CNS / Version: 0.5 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 10 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 29.7 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg15.7
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1
X-RAY DIFFRACTIONc_mcbond_it2
X-RAY DIFFRACTIONc_scbond_it3
X-RAY DIFFRACTIONc_mcangle_it3
X-RAY DIFFRACTIONc_scangle_it3.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.27 / % reflection Rfree: 9.8 % / Rfactor Rwork: 0.233

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