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- PDB-3s45: wild-type HIV-2 protease with antiviral drug amprenavir -

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Basic information

Entry
Database: PDB / ID: 3s45
Titlewild-type HIV-2 protease with antiviral drug amprenavir
ComponentsProtease
KeywordsHYDROLASE/HYDROLASE INHIBITOR / AMPRENAVIR / HIV/AIDS / drug resistance / aspartic protease / molecular recognition / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


aspartic-type endopeptidase activity / proteolysis / metal ion binding
Similarity search - Function
Retropepsin-like catalytic domain / Retropepsins / Retroviral aspartyl protease / Aspartyl protease, retroviral-type family profile. / Peptidase A2A, retrovirus, catalytic / Cathepsin D, subunit A; domain 1 / Acid Proteases / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Aspartic peptidase domain superfamily ...Retropepsin-like catalytic domain / Retropepsins / Retroviral aspartyl protease / Aspartyl protease, retroviral-type family profile. / Peptidase A2A, retrovirus, catalytic / Cathepsin D, subunit A; domain 1 / Acid Proteases / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Aspartic peptidase domain superfamily / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Chem-478 / IMIDAZOLE / Protease
Similarity search - Component
Biological speciesHuman immunodeficiency virus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.51 Å
AuthorsTie, Y.-F. / Wang, Y.-F. / Weber, I.T.
CitationJournal: Protein Sci. / Year: 2012
Title: Critical differences in HIV-1 and HIV-2 protease specificity for clinical inhibitors.
Authors: Tie, Y. / Wang, Y.F. / Boross, P.I. / Chiu, T.Y. / Ghosh, A.K. / Tozser, J. / Louis, J.M. / Harrison, R.W. / Weber, I.T.
History
DepositionMay 18, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 21, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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: Protease
B: Protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,14125
Polymers21,4572
Non-polymers1,68523
Water1,76598
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3410 Å2
ΔGint-21 kcal/mol
Surface area9900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.998, 30.986, 56.161
Angle α, β, γ (deg.)90.00, 91.66, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-1001-

HOH

21A-1002-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Protease


Mass: 10728.337 Da / Num. of mol.: 2 / Fragment: residues 514-612
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 2 / Strain: 11720 / Gene: pol / Plasmid: PET11A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q9W9R3, HIV-2 retropepsin

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Non-polymers , 6 types, 121 molecules

#2: Chemical ChemComp-NA / SODIUM ION


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


Mass: 35.453 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H5N2
#5: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Zn
#6: Chemical ChemComp-478 / {3-[(4-AMINO-BENZENESULFONYL)-ISOBUTYL-AMINO]-1-BENZYL-2-HYDROXY-PROPYL}-CARBAMIC ACID TETRAHYDRO-FURAN-3-YL ESTER / Amprenavir


Mass: 505.627 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C25H35N3O6S / Comment: medication*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 98 / 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: 2.15 Å3/Da / Density % sol: 42.74 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 1.5 M NaCl, 0.6 M imidazole/0.12 M Zinc Acetate Buffer at pH 6.0. 30% glycerol as cryoprotector, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.8 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Jun 15, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8 Å / Relative weight: 1
ReflectionResolution: 1.51→50 Å / Num. all: 25917 / Num. obs: 25917 / % possible obs: 90.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Biso Wilson estimate: 13.1 Å2 / Rmerge(I) obs: 0.081 / Net I/σ(I): 12.8
Reflection shellResolution: 1.51→1.56 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.255 / Mean I/σ(I) obs: 2.9 / Num. unique all: 1811 / % possible all: 63.3

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Processing

Software
NameClassification
HKL-2000data collection
AMoREphasing
SHELXL-97refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3EBZ

3ebz


Resolution: 1.51→10 Å / Num. parameters: 15542 / Num. restraintsaints: 19854 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER / Details: conjugage gradient minimization
RfactorNum. reflection% reflectionSelection details
Rfree0.246 1282 5 %RANDOM
Rwork0.183 ---
all0.1865 25801 --
obs0.183 25801 89.9 %-
Refine analyzeNum. disordered residues: 8 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 1669.7
Refinement stepCycle: LAST / Resolution: 1.51→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1510 0 81 98 1689
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.007
X-RAY DIFFRACTIONs_angle_d0.026
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0288
X-RAY DIFFRACTIONs_zero_chiral_vol0.039
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.052
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.008
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.004
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.036
X-RAY DIFFRACTIONs_approx_iso_adps0.072

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