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- PDB-5upj: HIV-2 PROTEASE/U99283 COMPLEX -

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Basic information

Entry
Database: PDB / ID: 5upj
TitleHIV-2 PROTEASE/U99283 COMPLEX
ComponentsHIV-2 PROTEASE
KeywordsHYDROLASE / ACID PROTEASE / HIV-2 PROTEASE-INHIBITOR COMPLEX / PROTEIN-SUBSTRATE INTERACTION / ASPARTYL PROTEASE
Function / homology
Function and homology information


HIV-2 retropepsin / 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 / host multivesicular body ...HIV-2 retropepsin / 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 / host multivesicular body / viral penetration into host nucleus / 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
gag protein p24 N-terminal 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 ...gag protein p24 N-terminal 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
Chem-UIN / Gag-Pol polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus 2
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsWatenpaugh, K.D. / Mulichak, A.M. / Finzel, B.C.
Citation
Journal: J.Med.Chem. / Year: 1995
Title: Use of medium-sized cycloalkyl rings to enhance secondary binding: discovery of a new class of human immunodeficiency virus (HIV) protease inhibitors.
Authors: Romines, K.R. / Watenpaugh, K.D. / Tomich, P.K. / Howe, W.J. / Morris, J.K. / Lovasz, K.D. / Mulichak, A.M. / Finzel, B.C. / Lynn, J.C. / Horng, M.-M. / Schwende, F.J. / Ruwart, M.J. / Zipp, ...Authors: Romines, K.R. / Watenpaugh, K.D. / Tomich, P.K. / Howe, W.J. / Morris, J.K. / Lovasz, K.D. / Mulichak, A.M. / Finzel, B.C. / Lynn, J.C. / Horng, M.-M. / Schwende, F.J. / Ruwart, M.J. / Zipp, G.L. / Chong, K.-T. / Dolak, L.A. / Toth, L.N. / Howard, G.M. / Rush, B.D. / Wilkinson, K.F. / Possert, P.L. / Dalga, R.J. / Hinshaw, R.R.
#1: Journal: J.Med.Chem. / Year: 1995
Title: Structure-based design of sulfonamide-substituted non-peptidic HIV protease inhibitors.
Authors: Skulnick, H.I. / Johnson, P.D. / Howe, W.J. / Tomich, P.K. / Chong, K.-T. / Watenpaugh, K.D. / Janakiraman, M.N. / Dolak, L.A. / Mcgrath, J.P. / Lynn, J.C. / Horng, M.-M. / Hinshaw, R.R. / ...Authors: Skulnick, H.I. / Johnson, P.D. / Howe, W.J. / Tomich, P.K. / Chong, K.-T. / Watenpaugh, K.D. / Janakiraman, M.N. / Dolak, L.A. / Mcgrath, J.P. / Lynn, J.C. / Horng, M.-M. / Hinshaw, R.R. / Zipp, G.L. / Ruwart, M.J. / Schwende, F.J. / Zhong, W.-Z. / Padbury, G.E. / Dalga, R.J. / Shiou, L. / Possert, P.L. / Rush, B.D. / Wilkinson, K.F. / Howard, G.M. / Toth, L.N. / Williams, M.G. / Kakuk, T.J. / Cole, S.L. / Zaya, R.M. / Lovasz, K.D. / Morris, J.K. / Romines, K.R. / Thaisrivongs, S. / Aristoff, P.A.
History
DepositionDec 10, 1996Processing site: BNL
Revision 1.0Apr 21, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 22, 2012Group: Database references
Revision 1.4Nov 3, 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 1.5Apr 3, 2024Group: 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: HIV-2 PROTEASE
B: HIV-2 PROTEASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,7373
Polymers21,4252
Non-polymers3121
Water5,621312
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4340 Å2
ΔGint-31 kcal/mol
Surface area9430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)33.382, 45.281, 133.359
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 HIV-2 PROTEASE / HUMAN IMMUNODEFICIENCY VIRUS TYPE 2 PROTEASE


Mass: 10712.315 Da / Num. of mol.: 2 / Mutation: K57L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 2 / Genus: Lentivirus / Production host: Escherichia coli (E. coli) / References: UniProt: P04584, HIV-1 retropepsin
#2: Chemical ChemComp-UIN / 5,6,7,8,9,10-HEXAHYDRO-4-HYDROXY-3-(1-PHENYLPROPYL)CYCLOOCTA[B]PYRAN-2-ONE


Mass: 312.403 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H24O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 312 / 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: 2.35 Å3/Da / Density % sol: 47.68 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 7.1
Details: CRYSTALS WERE GROWN AT ROOM TEMPERATURE IN 4-7 UL HANGING DROPS OF EQUAL VOLUMES OF PROTEIN AT 8-10 MG/L AND WELL SOLUTION OF 30-35%(W/V) PEG 4000 IN 0.1 M HEPES AND PH RANGE 6.8 - 7.6., pH ...Details: CRYSTALS WERE GROWN AT ROOM TEMPERATURE IN 4-7 UL HANGING DROPS OF EQUAL VOLUMES OF PROTEIN AT 8-10 MG/L AND WELL SOLUTION OF 30-35%(W/V) PEG 4000 IN 0.1 M HEPES AND PH RANGE 6.8 - 7.6., pH 7.1, vapor diffusion - hanging drop
PH range: 6.8-7.6 / Temp details: room temp
Crystal grow
*PLUS
pH: 7 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
18-10 mg/mlprotein1drop
230-35 %(w/v)PEG40001reservoir
30.1 MHEPES1reservoir
41-3 %n-butanol1reservoir

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: SIEMENS / Wavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: Feb 23, 1993
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→10 Å / Num. obs: 8579 / % possible obs: 90 % / Observed criterion σ(I): 0 / Redundancy: 4 % / Rmerge(I) obs: 0.064 / Net I/σ(I): 13.4
Reflection shellResolution: 2.3→2.44 Å / Redundancy: 3 % / Rmerge(I) obs: 0.303 / Mean I/σ(I) obs: 3.55 / % possible all: 73
Reflection
*PLUS
Num. measured all: 33887

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Processing

Software
NameClassification
MERLOTphasing
CEDARrefinement
XENGENdata reduction
XENGENdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: EARLIER STRUCTURE FROM SAME LABORATORY

Resolution: 2.3→10 Å / σ(F): 2 /
RfactorNum. reflection
Rwork0.182 -
obs-7695
Refinement stepCycle: LAST / Resolution: 2.3→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1500 0 23 312 1835
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.016
X-RAY DIFFRACTIONo_bond_d_na
X-RAY DIFFRACTIONo_bond_d_prot
X-RAY DIFFRACTIONo_angle_d
X-RAY DIFFRACTIONo_angle_d_na
X-RAY DIFFRACTIONo_angle_d_prot
X-RAY DIFFRACTIONo_angle_deg2.547
X-RAY DIFFRACTIONo_angle_deg_na
X-RAY DIFFRACTIONo_angle_deg_prot
X-RAY DIFFRACTIONo_dihedral_angle_d
X-RAY DIFFRACTIONo_dihedral_angle_d_na
X-RAY DIFFRACTIONo_dihedral_angle_d_prot
X-RAY DIFFRACTIONo_improper_angle_d
X-RAY DIFFRACTIONo_improper_angle_d_na
X-RAY DIFFRACTIONo_improper_angle_d_prot
X-RAY DIFFRACTIONo_mcbond_it
X-RAY DIFFRACTIONo_mcangle_it
X-RAY DIFFRACTIONo_scbond_it
X-RAY DIFFRACTIONo_scangle_it
Software
*PLUS
Name: CEDAR / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.189
Solvent computation
*PLUS
Displacement parameters
*PLUS

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