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- PDB-2hvp: THREE-DIMENSIONAL STRUCTURE OF ASPARTYL PROTEASE FROM HUMAN IMMUN... -

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Basic information

Entry
Database: PDB / ID: 2hvp
TitleTHREE-DIMENSIONAL STRUCTURE OF ASPARTYL PROTEASE FROM HUMAN IMMUNODEFICIENCY VIRUS HIV-1
ComponentsHIV-1 PROTEASE
KeywordsHYDROLASE(ACID PROTEINASE)
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 / 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
Similarity search - Domain/homology
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / Resolution: 3 Å
AuthorsNavia, M.A. / Fitzgerald, P.M.D. / Mckeever, B.M. / Springer, J.P.
Citation
Journal: Nature / Year: 1989
Title: Three-dimensional structure of aspartyl protease from human immunodeficiency virus HIV-1.
Authors: Navia, M.A. / Fitzgerald, P.M. / McKeever, B.M. / Leu, C.T. / Heimbach, J.C. / Herber, W.K. / Sigal, I.S. / Darke, P.L. / Springer, J.P.
#1: Journal: J.Biol.Chem. / Year: 1989
Title: Crystallization of the Aspartylprotease from the Human Immunodeficiency Virus, HIV-1
Authors: Mckeever, B.M. / Navia, M.A. / Fitzgerald, P.M.D. / Springer, J.P. / Leu, C.-T. / Heimbach, J.C. / Herber, W.K. / Sigal, I.S. / Darke, P.L.
History
DepositionApr 10, 1989Processing site: BNL
Revision 1.0Apr 19, 1989Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HIV-1 PROTEASE


Theoretical massNumber of molelcules
Total (without water)10,8311
Polymers10,8311
Non-polymers00
Water00
1
A: HIV-1 PROTEASE

A: HIV-1 PROTEASE


Theoretical massNumber of molelcules
Total (without water)21,6622
Polymers21,6622
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Unit cell
Length a, b, c (Å)50.290, 50.290, 106.800
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
DetailsTHE HIV-1 PROTEASE IS A DIMER. IN THE CRYSTAL THE TWO MONOMERS ARE RELATED BY A CRYSTALLOGRAPHIC TWO-FOLD AXIS. TO GENERATE THE SYMMETRY RELATED MONOMER, THE FOLLOWING TRANSFORMATION MUST BE APPLIED TO THE COORDINATES PRESENTED IN THIS ENTRY 0.0 -1.0 0.0 50.29 -1.0 0.0 0.0 50.29 0.0 0.0 -1.0 53.40

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Components

#1: Protein HIV-1 PROTEASE / Coordinate model: Cα atoms only


Mass: 10830.781 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Genus: Lentivirus / References: UniProt: P12497

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.12 Å3/Da / Density % sol: 60.52 %
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 7 / Method: vapor diffusion, hanging drop / Details: referred to J.Biol.Chem. 264,1919-1921
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
16 mg/mlprotein1drop
2100 mMimidazole/HCl1dropor NaMOPS/MOPS
3250 mM1dropNaCl
410 mMDTT1drop
53 mM1dropNaN3

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Data collection

Reflection
*PLUS
Highest resolution: 3 Å / Rmerge(I) obs: 0.063

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Processing

SoftwareName: CORELS / Classification: refinement
RefinementHighest resolution: 3 Å
Refinement stepCycle: LAST / Highest resolution: 3 Å /
ProteinNucleic acidLigandSolventTotal
Num. atoms94 0 0 0 94
Refinement
*PLUS
Highest resolution: 3 Å / Rfactor obs: 0.37
Solvent computation
*PLUS
Displacement parameters
*PLUS

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