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- PDB-3ggx: HIV Protease, pseudo-symmetric inhibitors -

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Basic information

Entry
Database: PDB / ID: 3ggx
TitleHIV Protease, pseudo-symmetric inhibitors
ComponentsV-1 protease
KeywordsHYDROLASE / HIV Protease / pseudo-symmetric inhibitors / Protease
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 / viral penetration into host nucleus / symbiont-mediated suppression of host gene expression / 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 / 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 / Reverse transcriptase domain / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase (RT) catalytic domain profile. / Retropepsins / Retroviral aspartyl protease / Aspartyl protease, retroviral-type family profile. / Peptidase A2A, retrovirus, catalytic / Retrovirus capsid, C-terminal / Retroviral matrix protein / Retrovirus capsid, N-terminal / zinc finger / Zinc knuckle / Cathepsin D, subunit A; domain 1 / Acid Proteases / 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
Chem-GGX / Gag-Pol polyprotein / V-1 protease
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsStoll, V.S.
CitationJournal: J.Med.Chem. / Year: 2009
Title: 2-Pyridyl P1'-substituted symmetry-based human immunodeficiency virus protease inhibitors (A-792611 and A-790742) with potential for convenient dosing and reduced side effects.
Authors: Degoey, D.A. / Grampovnik, D.J. / Flentge, C.A. / Flosi, W.J. / Chen, H.J. / Yeung, C.M. / Randolph, J.T. / Klein, L.L. / Dekhtyar, T. / Colletti, L. / Marsh, K.C. / Stoll, V. / Mamo, M. / ...Authors: Degoey, D.A. / Grampovnik, D.J. / Flentge, C.A. / Flosi, W.J. / Chen, H.J. / Yeung, C.M. / Randolph, J.T. / Klein, L.L. / Dekhtyar, T. / Colletti, L. / Marsh, K.C. / Stoll, V. / Mamo, M. / Morfitt, D.C. / Nguyen, B. / Schmidt, J.M. / Swanson, S.J. / Mo, H. / Kati, W.M. / Molla, A. / Kempf, D.J.
History
DepositionMar 2, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 26, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: V-1 protease
B: V-1 protease
C: V-1 protease
D: V-1 protease
E: V-1 protease
F: V-1 protease
G: V-1 protease
H: V-1 protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,70212
Polymers86,4308
Non-polymers3,2724
Water00
1
A: V-1 protease
B: V-1 protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,4263
Polymers21,6082
Non-polymers8181
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4050 Å2
ΔGint-24 kcal/mol
Surface area9520 Å2
MethodPISA
2
C: V-1 protease
D: V-1 protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,4263
Polymers21,6082
Non-polymers8181
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4100 Å2
ΔGint-25 kcal/mol
Surface area9280 Å2
MethodPISA
3
E: V-1 protease
F: V-1 protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,4263
Polymers21,6082
Non-polymers8181
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4020 Å2
ΔGint-24 kcal/mol
Surface area9360 Å2
MethodPISA
4
G: V-1 protease
H: V-1 protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,4263
Polymers21,6082
Non-polymers8181
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4000 Å2
ΔGint-23 kcal/mol
Surface area9470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.654, 195.569, 50.371
Angle α, β, γ (deg.)90.00, 91.19, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
V-1 protease


Mass: 10803.756 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: ORF / Plasmid: pBS27 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Q2G8, UniProt: P03366*PLUS
#2: Chemical
ChemComp-GGX / methyl [(1S)-1-{[(1R,3S,4S)-4-{[(2S)-3,3-dimethyl-2-{3-[(6-methylpyridin-2-yl)methyl]-2-oxo-2,3-dihydro-1H-imidazol-1-yl}butanoyl]amino}-3-hydroxy-5-phenyl-1-(4-pyridin-2-ylbenzyl)pentyl]carbamoyl}-2,2-dimethylpropyl]carbamate


Mass: 818.015 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C47H59N7O6

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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: 2.43 Å3/Da / Density % sol: 49.39 %
Crystal growMethod: vapor diffusion, hanging drop / Details: VAPOR DIFFUSION, HANGING DROP

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→97.78 Å / Num. obs: 19620

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Processing

Software
NameVersionClassification
HKL-2000data collection
AMoREphasing
REFMAC5.5.0066refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→42.65 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.868 / SU B: 13.781 / SU ML: 0.279 / Cross valid method: THROUGHOUT / ESU R Free: 0.409 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25459 1047 5.1 %RANDOM
Rwork0.20536 ---
obs0.20798 19620 91.49 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.789 Å2
Baniso -1Baniso -2Baniso -3
1-0.87 Å20 Å20.35 Å2
2--0.14 Å2-0 Å2
3----1 Å2
Refinement stepCycle: LAST / Resolution: 2.7→42.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6038 0 240 0 6278
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0226426
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9142.0318722
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6675784
X-RAY DIFFRACTIONr_dihedral_angle_2_deg43.24725.135222
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.983151128
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.281532
X-RAY DIFFRACTIONr_chiral_restr0.0960.21018
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0214908
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7071.53902
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.38926338
X-RAY DIFFRACTIONr_scbond_it2.10732524
X-RAY DIFFRACTIONr_scangle_it3.6594.52384
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.502 76 -
Rwork0.327 1453 -
obs--91.39 %

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