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- PDB-2hpf: COMPARISON OF THE STRUCTURES OF HIV-2 PROTEASE COMPLEXES IN THREE... -

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Entry
Database: PDB / ID: 2hpf
TitleCOMPARISON OF THE STRUCTURES OF HIV-2 PROTEASE COMPLEXES IN THREE CRYSTAL SPACE GROUPS WITH AN HIV-1 PROTEASE COMPLEX STRUCTURE
Components
  • HIV-2 PROTEASE
  • UNIDENTIFIED PEPTIDE FRAGMENT
KeywordsHYDROLASE(ACID PROTEASE)
Function / homology
Function and homology information


HIV-2 retropepsin / 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 ...HIV-2 retropepsin / 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 / 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 / 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 / Reverse transcriptase domain / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase (RT) catalytic domain profile. / Retrovirus capsid, C-terminal / 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
Biological speciesHuman immunodeficiency virus 2
MethodX-RAY DIFFRACTION / Resolution: 3 Å
AuthorsMulichak, A.M. / Watenpaugh, K.D.
Citation
Journal: To be Published
Title: Comparison of the Structures of HIV-2 Protease Complexes in Three Crystal Space Groups with an HIV-1 Protease Complex Structure
Authors: Mulichak, A.M. / Watenpaugh, K.D.
#1: Journal: J.Biol.Chem. / Year: 1993
Title: The Crystallographic Structure of the Protease from Human Immunodeficiency Virus Type 2 with Two Synthetic Peptidic Transition State Analog Inhibitors
Authors: Mulichak, A.M. / Hui, J.O. / Tomasselli, A.G. / Heinrikson, R.L. / Curry, K.A. / Tomich, C.-S. / Thaisrivongs, S. / Sawyer, T.K. / Watenpaugh, K.D.
History
DepositionSep 21, 1994Processing site: BNL
Revision 1.0Oct 15, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4Feb 14, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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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
S: UNIDENTIFIED PEPTIDE FRAGMENT


Theoretical massNumber of molelcules
Total (without water)22,1233
Polymers22,1233
Non-polymers00
Water1,36976
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)80.170, 80.170, 71.140
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein HIV-2 PROTEASE


Mass: 10712.315 Da / Num. of mol.: 2
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
#2: Protein/peptide UNIDENTIFIED PEPTIDE FRAGMENT


Mass: 698.854 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 76 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHERE IS A PEPTIDE FRAGMENT IN THE SUBSTRATE BINDING POCKET. BECAUSE THE SIDE GROUPS ARE NOT KNOWN ...THERE IS A PEPTIDE FRAGMENT IN THE SUBSTRATE BINDING POCKET. BECAUSE THE SIDE GROUPS ARE NOT KNOWN FOR CERTAIN, THE RESIDUES HAVE ALL BEEN REPRESENTED AS "UNK". THERE ARE COORDINATES PRESENT FOR FOUR OR FIVE ATOMS OF EACH OF THESE RESIDUES (EACH CORRESPONDING TO THE ATOMS OF A GLYCIN OR ALANINE.)

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.98 Å3/Da / Density % sol: 58.75 %

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 3→40 Å / Num. obs: 5337 / % possible obs: 99 % / Observed criterion σ(F): 0

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementResolution: 3→10 Å / σ(F): 2
Details: ATOMS WITH B-FACTORS GREATER THAN 70.0 A**2 MAY BE CONSIDERED TO BE DISORDERED OR NOT SEEN IN THE ELECTRON DENSITY MAPS.
RfactorNum. reflection
obs0.144 3758
Refinement stepCycle: LAST / Resolution: 3→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1546 0 0 76 1622

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