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- PDB-3hlo: Crystal structure of chemically synthesized 'covalent dimer' [Gly... -

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Basic information

Entry
Database: PDB / ID: 3hlo
TitleCrystal structure of chemically synthesized 'covalent dimer' [Gly51/D-Ala51']HIV-1 protease
Components'covalent dimer' [Gly51/D-Ala51'] HIV-1 protease
KeywordsHYDROLASE/HYDROLASE INHIBITOR / beta barrel / HYDROLASE / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / RNA stem-loop binding ...HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / RNA stem-loop binding / viral penetration into host nucleus / host multivesicular body / 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 / aspartic-type endopeptidase activity / Hydrolases; Acting on ester bonds / DNA-directed DNA polymerase activity / symbiont-mediated suppression of host gene expression / viral translational frameshifting / lipid binding / symbiont entry into host cell / host cell nucleus / host cell plasma membrane / virion membrane / structural molecule activity / 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 / Matrix protein, lentiviral and alpha-retroviral, N-terminal / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / RNase H type-1 domain profile. / Ribonuclease H domain / Retropepsins / Retroviral aspartyl protease / Aspartyl protease, retroviral-type family profile. / Peptidase A2A, retrovirus, catalytic / Retrovirus capsid, C-terminal / Reverse transcriptase domain / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase (RT) catalytic domain profile. / Retroviral matrix protein / Cathepsin D, subunit A; domain 1 / Acid Proteases / Retrovirus capsid, N-terminal / zinc finger / Zinc knuckle / Zinc finger, CCHC-type superfamily / Zinc finger, CCHC-type / Zinc finger CCHC-type profile. / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Aspartic peptidase domain superfamily / Ribonuclease H superfamily / Ribonuclease H-like superfamily / Reverse transcriptase/Diguanylate cyclase domain / DNA/RNA polymerase superfamily / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
N-{(2S)-2-[(N-acetyl-L-threonyl-L-isoleucyl)amino]hexyl}-L-norleucyl-L-glutaminyl-N~5~-[amino(iminio)methyl]-L-ornithinamide / Chem-2NC / Gag-Pol polyprotein
Similarity search - Component
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsTorbeev, V.Y. / Kent, S.B.H.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2011
Title: Protein conformational dynamics in the mechanism of HIV-1 protease catalysis.
Authors: Torbeev, V.Y. / Raghuraman, H. / Hamelberg, D. / Tonelli, M. / Westler, W.M. / Perozo, E. / Kent, S.B.
History
DepositionMay 27, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 27, 2011Provider: repository / Type: Initial release
Revision 1.1Jan 11, 2012Group: Database references
Revision 1.2Dec 12, 2012Group: Other
Revision 1.3Mar 26, 2025Group: 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

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Assembly

Deposited unit
A: 'covalent dimer' [Gly51/D-Ala51'] HIV-1 protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,6772
Polymers21,9061
Non-polymers7711
Water2,540141
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)51.341, 58.059, 61.368
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein 'covalent dimer' [Gly51/D-Ala51'] HIV-1 protease


Mass: 21905.678 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: total chemical synthesis / References: UniProt: P03369*PLUS, HIV-1 retropepsin
#2: Chemical ChemComp-2NC / N-{(2S)-2-[(N-acetyl-L-threonyl-L-isoleucyl)amino]hexyl}-L-norleucyl-L-glutaminyl-N~5~-[amino(iminio)methyl]-L-ornithinamide / p2/NC


Type: peptide-like, Peptide-like / Class: Inhibitor / Mass: 770.983 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C35H68N11O8
References: N-{(2S)-2-[(N-acetyl-L-threonyl-L-isoleucyl)amino]hexyl}-L-norleucyl-L-glutaminyl-N~5~-[amino(iminio)methyl]-L-ornithinamide
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 141 / 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: 2.09 Å3/Da / Density % sol: 41.08 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.1 M citrate, 0.2 M sodium phosphate, 30% (v/v) ammonium sulfate, 10% (v/v) DMSO, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9002 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 26, 2007
Details: bent conical Si-mirror (Rh coating); bent Ge(111) monochromator
RadiationMonochromator: bent Ge(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9002 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. all: 25025 / Num. obs: 24925 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.3 % / Rmerge(I) obs: 0.047 / Net I/σ(I): 38.3
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.354 / Mean I/σ(I) obs: 6.61 / Num. unique all: 2450 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→20 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.952 / SU B: 2.278 / SU ML: 0.062 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.099 / ESU R Free: 0.098 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22148 1263 5.1 %RANDOM
Rwork0.18777 ---
obs0.18948 23595 99.59 %-
all-23692 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 25.329 Å2
Baniso -1Baniso -2Baniso -3
1-0.13 Å20 Å20 Å2
2--0 Å20 Å2
3----0.13 Å2
Refinement stepCycle: LAST / Resolution: 1.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1544 0 53 141 1738
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0221628
X-RAY DIFFRACTIONr_angle_refined_deg1.6911.9862201
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8815204
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.53824.91559
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.25415288
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.228159
X-RAY DIFFRACTIONr_chiral_restr0.1260.2258
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021174
X-RAY DIFFRACTIONr_nbd_refined0.20.2672
X-RAY DIFFRACTIONr_nbtor_refined0.3160.21117
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1430.2108
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1740.238
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1160.28
X-RAY DIFFRACTIONr_mcbond_it1.2171.51065
X-RAY DIFFRACTIONr_mcangle_it1.88921672
X-RAY DIFFRACTIONr_scbond_it2.6783636
X-RAY DIFFRACTIONr_scangle_it4.0994.5529
LS refinement shellResolution: 1.597→1.638 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.28 91 -
Rwork0.216 1698 -
obs--99.55 %

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