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- PDB-2mip: CRYSTAL STRUCTURE OF HUMAN IMMUNODEFICIENCY VIRUS (HIV) TYPE 2 PR... -

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Basic information

Entry
Database: PDB / ID: 2mip
TitleCRYSTAL STRUCTURE OF HUMAN IMMUNODEFICIENCY VIRUS (HIV) TYPE 2 PROTEASE IN COMPLEX WITH A REDUCED AMIDE INHIBITOR AND COMPARISON WITH HIV-1 PROTEASE STRUCTURES
Components
  • HIV-2 PROTEASE
  • INHIBITOR BI-LA-398
KeywordsHYDROLASE/HYDROLASE INHIBITOR / ACID PROTEINASE / HYDROLASE-HYDROLASE INHIBITOR complex
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 / symbiont-mediated suppression of host gene expression ...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 / symbiont-mediated suppression of host gene expression / 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 / Hydrolases; Acting on ester bonds / aspartic-type endopeptidase activity / DNA-directed DNA polymerase activity / symbiont entry into host cell / viral translational frameshifting / lipid binding / host cell nucleus / host cell plasma membrane / structural molecule activity / virion membrane / 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 / RNase H type-1 domain profile. / Ribonuclease H domain / Matrix protein, lentiviral and alpha-retroviral, N-terminal / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / Reverse transcriptase domain / Reverse transcriptase (RT) catalytic domain profile. / Retropepsins / Retroviral aspartyl protease / Aspartyl protease, retroviral-type family profile. / Peptidase A2A, retrovirus, catalytic / Reverse transcriptase (RNA-dependent DNA polymerase) / Retroviral matrix protein / Retrovirus capsid, C-terminal / Retrovirus capsid, N-terminal / zinc finger / Zinc knuckle / Zinc finger, CCHC-type superfamily / Cathepsin D, subunit A; domain 1 / Acid Proteases / Zinc finger, CCHC-type / Zinc finger CCHC-type profile. / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Ribonuclease H superfamily / Aspartic peptidase domain 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: 2.2 Å
AuthorsTong, L. / Pav, S. / Pargellis, C. / Do, F. / Lamarre, D. / Anderson, P.C.
CitationJournal: 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
DepositionJun 3, 1993Processing site: BNL
Revision 1.0Oct 31, 1993Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Structure summary / Version format compliance
Revision 1.3Jul 17, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Refinement description
Category: pdbx_database_status / software / struct_conn
Item: _pdbx_database_status.process_site / _software.classification / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Aug 14, 2019Group: Data collection / Refinement description / Category: software / Item: _software.classification
Revision 1.5Oct 9, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_comp_id / _struct_conn.ptnr2_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HIV-2 PROTEASE
B: HIV-2 PROTEASE
C: HIV-2 PROTEASE
D: HIV-2 PROTEASE
E: INHIBITOR BI-LA-398
F: INHIBITOR BI-LA-398
G: INHIBITOR BI-LA-398
H: INHIBITOR BI-LA-398


Theoretical massNumber of molelcules
Total (without water)45,9738
Polymers45,9738
Non-polymers00
Water1,62190
1
A: HIV-2 PROTEASE
B: HIV-2 PROTEASE
E: INHIBITOR BI-LA-398
G: INHIBITOR BI-LA-398


Theoretical massNumber of molelcules
Total (without water)22,9874
Polymers22,9874
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: HIV-2 PROTEASE
D: HIV-2 PROTEASE
F: INHIBITOR BI-LA-398
H: INHIBITOR BI-LA-398


Theoretical massNumber of molelcules
Total (without water)22,9874
Polymers22,9874
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.100, 55.100, 138.900
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43
Atom site foot note1: THERE IS A PSI LINKAGE (PHE 3-PSI(CH2NH)-LEU 4) IN THE INHIBITOR.

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Components

#1: Protein
HIV-2 PROTEASE


Mass: 10728.337 Da / Num. of mol.: 4
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
INHIBITOR BI-LA-398


Mass: 764.931 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 90 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.29 Å3/Da / Density % sol: 46.34 %
Crystal grow
*PLUS
pH: 7.4 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.UnitCommon nameCrystal-IDSol-IDChemical formula
20.02 %1dropNaN3
34-6 %DMSO1reservoir
1mg/mlprotein1drop

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2.2 Å / Num. obs: 18007 / Num. measured all: 85564 / Rmerge(I) obs: 0.066

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Processing

Software
NameClassification
X-PLORmodel building
TNTrefinement
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2.2→6 Å / σ(F): 2 /
RfactorNum. reflection
Rwork0.176 -
obs0.176 16845
Refinement stepCycle: LAST / Resolution: 2.2→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3236 0 0 90 3326
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.018
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_deg2.81
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/TNT / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.176
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_d / Dev ideal: 2.81
LS refinement shell
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 2.3 Å / Num. reflection obs: 1665 / Rfactor all: 25

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