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- PDB-1ida: CRYSTAL STRUCTURES OF HIV-2 PROTEASE IN COMPLEX WITH INHIBITORS C... -

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Basic information

Entry
Database: PDB / ID: 1ida
TitleCRYSTAL STRUCTURES OF HIV-2 PROTEASE IN COMPLEX WITH INHIBITORS CONTAINING THE HYDROXYETHYLAMINE DIPEPTIDE ISOSTERE
ComponentsProtease
KeywordsHYDROLASE/HYDROLASE INHIBITOR / ACID PROTEINASE / AIDS / Protease / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


HIV-2 retropepsin / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / DNA integration / host multivesicular body / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / RNA stem-loop binding ...HIV-2 retropepsin / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / DNA integration / host multivesicular body / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / RNA stem-loop binding / 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
N-[(1R)-1-{[(1S,2S)-1-benzyl-3-{(2R,4S)-2-(tert-butylcarbamoyl)-4-[(pyridin-3-ylmethyl)sulfanyl]piperidin-1-yl}- 2-hydroxypropyl]carbamoyl}-2-methylpropyl]quinoline-2-carboxamide / Chem-0PO / Gag-Pol polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus type 2
MethodX-RAY DIFFRACTION / Resolution: 1.7 Å
AuthorsTong, L. / Anderson, P.C.
Citation
Journal: Structure / Year: 1995
Title: Crystal structures of HIV-2 protease in complex with inhibitors containing the hydroxyethylamine dipeptide isostere.
Authors: Tong, L. / Pav, S. / Mui, S. / Lamarre, D. / Yoakim, C. / Beaulieu, P. / Anderson, P.C.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 1993
Title: Crystal Structure of Human Immunodeficiency Virus (HIV) Type 2 Protease in Complex with a Reduced Amide Inhibitor and Comparison with HIV-1 Protease Structures
Authors: Tong, L. / Pav, S. / Pargellis, C. / Do, F. / Lamarre, D. / Anderson, P.C.
History
DepositionOct 19, 1994Processing site: BNL
Revision 1.0Jan 26, 1995Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Source and taxonomy / Structure summary / Version format compliance
Revision 1.3Dec 12, 2012Group: Other
Revision 1.4Jul 17, 2019Group: Data collection / Other / Refinement description / Category: pdbx_database_status / software
Item: _pdbx_database_status.process_site / _software.classification
Revision 1.5Aug 14, 2019Group: Data collection / Refinement description / Category: software / Item: _software.classification
Revision 1.6Feb 7, 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: Protease
B: Protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,1823
Polymers21,4572
Non-polymers7251
Water2,036113
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5480 Å2
ΔGint-15 kcal/mol
Surface area9200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.600, 62.600, 115.800
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Protease / Retropepsin / PR


Mass: 10728.337 Da / Num. of mol.: 2 / Fragment: rsidues 514-622
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus type 2 / Genus: Lentivirus / Gene: gag-pol / Production host: Escherichia coli (E. coli) / References: UniProt: P04584, HIV-2 retropepsin
#2: Chemical ChemComp-0PO / N-[(1R)-1-{[(1S,2S)-1-benzyl-3-{(2R,4S)-2-(tert-butylcarbamoyl)-4-[(pyridin-3-ylmethyl)sulfanyl]piperidin-1-yl}-2-hydroxypropyl]carbamoyl}-2-methylpropyl]quinoline-2-carboxamide


Type: peptide-like, Peptide-like / Class: Inhibitor / Mass: 724.954 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C41H52N6O4S
References: N-[(1R)-1-{[(1S,2S)-1-benzyl-3-{(2R,4S)-2-(tert-butylcarbamoyl)-4-[(pyridin-3-ylmethyl)sulfanyl]piperidin-1-yl}- 2-hydroxypropyl]carbamoyl}-2-methylpropyl]quinoline-2-carboxamide
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 113 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.64 Å3/Da / Density % sol: 53.45 %
Crystal grow
*PLUS
pH: 5.4 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
16 mg/mlprotein1drop
210 %(v/v)phosphate1drop
30.02 %(w/v)1dropNaN3
40.3-0.5 M1reservoirNaCl
50.1 Msodium acetate1reservoir
60.02 %(w/v)1reservoirNaN3

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Num. obs: 22017 / % possible obs: 80 % / Observed criterion σ(F): 2

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Processing

Software
NameClassification
X-PLORmodel building
TNTrefinement
X-PLORrefinement
X-PLORphasing
RefinementResolution: 1.7→6 Å / σ(F): 2 /
RfactorNum. reflection
Rwork0.196 -
obs0.196 22017
Refinement stepCycle: LAST / Resolution: 1.7→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1510 0 52 113 1675
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.017
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg2.6
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.196
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_d / Dev ideal: 2.6

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