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- PDB-1heg: The crystal structures at 2.2 angstroms resolution of hydroxyethy... -

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Basic information

Entry
Database: PDB / ID: 1heg
TitleThe crystal structures at 2.2 angstroms resolution of hydroxyethylene-based inhibitors bound to human immunodeficiency virus type 1 protease show that the inhibitors are present in two distinct orientations
ComponentsHIV-1 PROTEASE
KeywordsHYDROLASE/HYDROLASE INHIBITOR / HYDROLASE-HYDROLASE INHIBITOR COMPLEX / 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 / host multivesicular body / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency ...HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / 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
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 / Reverse transcriptase domain / Retrovirus capsid, C-terminal / 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
Ala-Ala-Phe.psi.[CH(OH)CH2]Gly-Val-Val-OCH3 / Chem-PSI / Gag-Pol polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / Resolution: 2.2 Å
AuthorsMurthy, K. / Winborne, E.L. / Minnich, M.D. / Culp, J.S. / Debouck, C.
CitationJournal: J.Biol.Chem. / Year: 1992
Title: The crystal structures at 2.2-A resolution of hydroxyethylene-based inhibitors bound to human immunodeficiency virus type 1 protease show that the inhibitors are present in two distinct orientations.
Authors: Murthy, K.H. / Winborne, E.L. / Minnich, M.D. / Culp, J.S. / Debouck, C.
History
DepositionSep 21, 1992Processing site: BNL
Revision 1.0May 31, 1994Provider: 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 / Structure summary / Version format compliance
Revision 1.3Dec 12, 2012Group: Other
Revision 1.4Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.5Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.6Mar 13, 2024Group: Source and taxonomy / Structure summary / Category: entity / pdbx_entity_src_syn / Item: _entity.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
E: HIV-1 PROTEASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,3642
Polymers10,7871
Non-polymers5781
Water59433
1
E: HIV-1 PROTEASE
hetero molecules

E: HIV-1 PROTEASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,7294
Polymers21,5732
Non-polymers1,1552
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation9_555-x,-x+y,-z+2/31
Buried area4300 Å2
ΔGint-29 kcal/mol
Surface area9780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.140, 64.140, 84.240
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Atom site foot note1: RESIDUES PHE I 203, OHE I 203A, AND GLY I 204 REPRESENT PHE-PSI(CHOH-CH2)-GLY. THUS ATOMS C AND N OF PHE I 203 AND ATOM N OF GLY I 204 ARE NOT PRESENT AND ARE REPLACED BY THE ATOMS OF THE HET GROUP OHE.

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Components

#1: Protein HIV-1 PROTEASE


Mass: 10786.663 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Genus: Lentivirus / Production host: Escherichia coli (E. coli) / References: UniProt: P03366
#2: Chemical ChemComp-PSI / methyl N-{(4S,5S)-5-[(L-alanyl-L-alanyl)amino]-4-hydroxy-6-phenylhexanoyl}-L-valyl-L-valinate / SKF 107457


Type: peptide-like, Peptide-like / Class: Enzyme inhibitor / Mass: 577.713 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C29H47N5O7 / Details: Synthetic peptide / References: Ala-Ala-Phe.psi.[CH(OH)CH2]Gly-Val-Val-OCH3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 33 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsTHE SCISSILE BOND IN THE INHIBITOR PSI IS REPLACED BY A HYDROXYETHYLENE ISOSTERE (CHOH-CH2) THE ...THE SCISSILE BOND IN THE INHIBITOR PSI IS REPLACED BY A HYDROXYETHYLENE ISOSTERE (CHOH-CH2) THE INHIBITOR IS SMALL ENOUGH TO BE ENTIRELY CONTAINED WITHIN THE ACTIVE SITE OF THE ENZYME AND, THEREFORE, DOES NOT CONTRIBUTE TO INTER-DIMER CONTACTS.OF THE TWO POSSIBLE ORIENTATIONS OF THE INHIBITOR, NEITHER IS THERMODYNAMICALLY PREFERRED. IN THE CRYSTAL STRUCTURE, THEREFORE, BOTH ARE REPRESENTED EQUALLY.
Sequence detailsTHIS VARIANT OF THE HIV 1 PROTEASE HAS ASN 36 AS CONFIRMED BY INSPECTION OF THE ELECTRON DENSITY. ...THIS VARIANT OF THE HIV 1 PROTEASE HAS ASN 36 AS CONFIRMED BY INSPECTION OF THE ELECTRON DENSITY. SEE REFERENCES 14, 15, AND 16 IN J.BIOL.CHEM. V.267:22770, (1992).

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.19 Å3/Da / Density % sol: 43.96 %
Crystal grow
*PLUS
pH: 5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
114-24 %satammonium sulfate1reservoir
2200 mMacetate1reservoir
450 mMsodium acetate1drop
5200 mMsodium chloride1drop
65 mMdithiothreitol1drop
72 mMEDTA1drop
3protein-inhibitor complex1drop0.002ml

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementResolution: 2.2→5 Å / σ(I): 2 /
RfactorNum. reflection
Rwork0.186 -
obs0.186 3597
Refinement stepCycle: LAST / Resolution: 2.2→5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms758 0 41 33 832
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.020.025
X-RAY DIFFRACTIONp_angle_d0.0430.05
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0560.06
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr0.1990.2
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor1.52
X-RAY DIFFRACTIONp_staggered_tor25.115
X-RAY DIFFRACTIONp_orthonormal_tor27.225
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: PROLSQ / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.186
Solvent computation
*PLUS
Displacement parameters
*PLUS

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