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- PDB-1hsh: CRYSTAL STRUCTURE AT 1.9 ANGSTROMS RESOLUTION OF HUMAN IMMUNODEFI... -

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Basic information

Entry
Database: PDB / ID: 1hsh
TitleCRYSTAL STRUCTURE AT 1.9 ANGSTROMS RESOLUTION OF HUMAN IMMUNODEFICIENCY VIRUS (HIV) II PROTEASE COMPLEXED WITH L-735,524, AN ORALLY BIOAVAILABLE INHIBITOR OF THE HIV PROTEASES
ComponentsHIV-II PROTEASE
KeywordsHYDROLASE / HYDROLASE (ACID PROTEINASE)
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-[2(R)-HYDROXY-1(S)-INDANYL]-5-[(2(S)-TERTIARY / Gag-Pol polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus 2
MethodX-RAY DIFFRACTION / Resolution: 1.9 Å
AuthorsChen, Z.
CitationJournal: J.Biol.Chem. / Year: 1994
Title: Crystal structure at 1.9-A resolution of human immunodeficiency virus (HIV) II protease complexed with L-735,524, an orally bioavailable inhibitor of the HIV proteases.
Authors: Chen, Z. / Li, Y. / Chen, E. / Hall, D.L. / Darke, P.L. / Culberson, C. / Shafer, J.A. / Kuo, L.C.
History
DepositionMar 31, 1995Processing site: BNL
Revision 1.0Apr 3, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 9, 2014Group: Source and taxonomy
Revision 1.4Feb 7, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _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: HIV-II PROTEASE
B: HIV-II PROTEASE
C: HIV-II PROTEASE
D: HIV-II PROTEASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,1416
Polymers42,9134
Non-polymers1,2282
Water3,207178
1
A: HIV-II PROTEASE
B: HIV-II PROTEASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,0703
Polymers21,4572
Non-polymers6141
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4790 Å2
ΔGint-14 kcal/mol
Surface area9320 Å2
MethodPISA
2
C: HIV-II PROTEASE
D: HIV-II PROTEASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,0703
Polymers21,4572
Non-polymers6141
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4900 Å2
ΔGint-13 kcal/mol
Surface area9550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.520, 57.500, 63.250
Angle α, β, γ (deg.)90.00, 95.14, 90.00
Int Tables number4
Space group name H-MP1211
Atom site foot note1: ILE A 15 - GLU A 16 OMEGA = 249.95 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
2: GLU A 16 - GLY A 17 OMEGA = 211.98 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
3: GLU A 37 - LEU A 38 OMEGA = 210.03 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION

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Components

#1: Protein
HIV-II PROTEASE


Mass: 10728.337 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: ROD ISOLATE / Source: (gene. exp.) Human immunodeficiency virus 2 / Production host: Escherichia coli (E. coli)
References: UniProt: P04584, Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases
#2: Chemical ChemComp-MK1 / N-[2(R)-HYDROXY-1(S)-INDANYL]-5-[(2(S)-TERTIARY BUTYLAMINOCARBONYL)-4(3-PYRIDYLMETHYL)PIPERAZINO]-4(S)-HYDROXY-2(R)-PHENYLMETHYLPENTANAMIDE / INDINAVIR


Mass: 613.789 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C36H47N5O4 / Comment: medication*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 178 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsL-735,524 IS N-[2(R)-HYDROXY-1(S)-INDANYL]-5-[(2(S)- TERTIARY- BUTYLAMINOCARBONYL)-4(3- ...L-735,524 IS N-[2(R)-HYDROXY-1(S)-INDANYL]-5-[(2(S)- TERTIARY- BUTYLAMINOCARBONYL)-4(3-PYRIDYLMETHYL)PIPERAZINO] -4(S)-HYDROXY- 2(R)- PHENYLMETHLPENTANAMIDE MONOHYDRATE.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.38 Å3/Da / Density % sol: 48.41 %
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 7.5 / Method: other
Components of the solutions
*PLUS
IDCrystal-ID
11
21
31

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementRfactor Rwork: 0.194 / Rfactor obs: 0.194 / Highest resolution: 1.9 Å
Refinement stepCycle: LAST / Highest resolution: 1.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3016 0 90 178 3284
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.012
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_deg1.7
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
Refinement
*PLUS
Lowest resolution: 6 Å / Num. reflection obs: 22768
Solvent computation
*PLUS
Displacement parameters
*PLUS

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