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- PDB-2a1e: High resolution structure of HIV-1 PR with TS-126 -

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Basic information

Entry
Database: PDB / ID: 2a1e
TitleHigh resolution structure of HIV-1 PR with TS-126
ComponentsPol polyprotein
KeywordsHYDROLASE / HIV PR / PEPTIDOMIMETIC INHIBITOR / STEREOISOMER / SCREENING A MIXTURE
Function / homology
Function and homology information


HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / host multivesicular body / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency ...HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / host multivesicular body / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / symbiont-mediated suppression of host gene expression / viral penetration into host nucleus / RNA stem-loop binding / RNA-directed DNA polymerase activity / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / host cell / viral nucleocapsid / DNA recombination / DNA-directed DNA polymerase / Hydrolases; Acting on ester bonds / aspartic-type endopeptidase activity / DNA-directed DNA polymerase activity / symbiont entry into host cell / viral translational frameshifting / lipid binding / host cell nucleus / host cell plasma membrane / structural molecule activity / virion membrane / proteolysis / DNA binding / zinc ion binding / membrane
Similarity search - Function
Reverse transcriptase connection / Reverse transcriptase connection domain / Reverse transcriptase thumb / Reverse transcriptase thumb domain / Integrase Zinc binding domain / Zinc finger integrase-type profile. / Integrase-like, N-terminal / Integrase DNA binding domain / Integrase, C-terminal domain superfamily, retroviral / Integrase, N-terminal zinc-binding domain ...Reverse transcriptase connection / Reverse transcriptase connection domain / Reverse transcriptase thumb / Reverse transcriptase thumb domain / Integrase Zinc binding domain / Zinc finger integrase-type profile. / Integrase-like, N-terminal / Integrase DNA binding domain / Integrase, C-terminal domain superfamily, retroviral / Integrase, N-terminal zinc-binding domain / Integrase, C-terminal, retroviral / Integrase DNA binding domain profile. / Immunodeficiency lentiviral matrix, N-terminal / gag gene protein p17 (matrix protein) / RNase H / Integrase core domain / Integrase, catalytic core / Integrase catalytic domain profile. / Retropepsin-like catalytic domain / RNase H type-1 domain profile. / Ribonuclease H domain / Matrix protein, lentiviral and alpha-retroviral, N-terminal / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / Reverse transcriptase domain / Reverse transcriptase (RT) catalytic domain profile. / Retropepsins / Retroviral aspartyl protease / Aspartyl protease, retroviral-type family profile. / Peptidase A2A, retrovirus, catalytic / Reverse transcriptase (RNA-dependent DNA polymerase) / Retroviral matrix protein / Retrovirus capsid, C-terminal / Retrovirus capsid, N-terminal / zinc finger / Zinc knuckle / Zinc finger, CCHC-type superfamily / Cathepsin D, subunit A; domain 1 / Acid Proteases / Zinc finger, CCHC-type / Zinc finger CCHC-type profile. / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Ribonuclease H superfamily / Aspartic peptidase domain superfamily / Ribonuclease H-like superfamily / Reverse transcriptase/Diguanylate cyclase domain / DNA/RNA polymerase superfamily / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
ACETATE ION / Chem-IPF / Gag-Pol polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsDemitri, N. / Geremia, S. / Randaccio, L. / Wuerges, J. / Benedetti, F. / Berti, F. / Dinon, F. / Campaner, P. / Tell, G.
CitationJournal: Chemmedchem / Year: 2006
Title: A potent HIV protease inhibitor identified in an epimeric mixture by high-resolution protein crystallography.
Authors: Geremia, S. / Demitri, N. / Wuerges, J. / Benedetti, F. / Berti, F. / Tell, G. / Randaccio, L.
History
DepositionJun 20, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 21, 2006Provider: repository / Type: Initial release
Revision 1.1Oct 21, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Nov 10, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Pol polyprotein
B: Pol polyprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,04613
Polymers21,4812
Non-polymers1,56411
Water4,900272
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7010 Å2
ΔGint-38 kcal/mol
Surface area9350 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)57.269, 84.956, 46.061
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11B-478-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Pol polyprotein / HIV-1 PROTEASE


Mass: 10740.677 Da / Num. of mol.: 2 / Fragment: Protease / Mutation: Q7K/L33I/L63I/C67A/C95A
Source method: isolated from a genetically manipulated source
Details: IPF: Pseudo-esapeptide built up from a di-hydroxyethylene Phe-Pro isostere core, coupled with 2 equivalents of Ac-NH-Trp-Val-OH.
Source: (gene. exp.) Human immunodeficiency virus 1 / Genus: Lentivirus / Gene: GAG-POL / Plasmid: PET11A / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P03367, HIV-1 retropepsin

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Non-polymers , 7 types, 283 molecules

#2: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#6: Chemical ChemComp-IPF / N-ACETYLTRYPTOPHYL-N~1~-{3-[1-(N-ACETYLTRYPTOPHYLVALYL)PYRROLIDIN-2-YL]-1-BENZYL-2,3-DIHYDROXYPROPYL}VALINAMIDE


Mass: 905.092 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C50H64N8O8
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 272 / 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: 2.61 Å3/Da / Density % sol: 52.81 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: ammonium sulfate, DMSO, sodium acetate, pH 6, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1.2 / Wavelength: 1.2 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 3, 2004 / Details: MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.21
21.21
ReflectionResolution: 1.3→10 Å / Num. all: 55106 / Num. obs: 55106 / % possible obs: 98.6 % / Redundancy: 2.7 % / Rmerge(I) obs: 0.061 / Net I/σ(I): 10
Reflection shellResolution: 1.3→1.37 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.408 / Mean I/σ(I) obs: 2.5 / % possible all: 98.3

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
SHELXL-97refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1S6G

1s6g
PDB Unreleased entry


Resolution: 1.3→10 Å / Num. parameters: 15541 / Num. restraintsaints: 18509 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY 3.3%
RfactorNum. reflection% reflectionSelection details
Rfree0.2013 2761 -RANDOM
Rwork0.1558 ---
obs0.1558 52307 98.6 %-
all-55106 --
Displacement parametersBiso mean: 19.49 Å2
Refine analyzeNum. disordered residues: 8 / Occupancy sum hydrogen: 1679 / Occupancy sum non hydrogen: 1849
Refinement stepCycle: LAST / Resolution: 1.3→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1512 0 102 272 1886
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.013
X-RAY DIFFRACTIONs_angle_d0.033
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0302
X-RAY DIFFRACTIONs_zero_chiral_vol0.067
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.069
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.019
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.004
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.053
X-RAY DIFFRACTIONs_approx_iso_adps0

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