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- PDB-8hvp: STRUCTURE AT 2.5-ANGSTROMS RESOLUTION OF CHEMICALLY SYNTHESIZED H... -

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Basic information

Entry
Database: PDB / ID: 8hvp
TitleSTRUCTURE AT 2.5-ANGSTROMS RESOLUTION OF CHEMICALLY SYNTHESIZED HUMAN IMMUNODEFICIENCY VIRUS TYPE 1 PROTEASE COMPLEXED WITH A HYDROXYETHYLENE*-BASED INHIBITOR
Components
  • HIV-1 PROTEASE
  • INHIBITOR VAL-SER-GLN-ASN-LEU-PSI(CH(OH)-CH2)-VAL-ILE-VAL (U-85548E)
KeywordsHYDROLASE/HYDROLASE INHIBITOR / ACID PROTEINASE / HYDROLASE-HYDROLASE INHIBITOR COMPLEX
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 / telomerase activity / viral penetration into host nucleus / RNA stem-loop binding / 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 / symbiont entry into host cell / viral translational frameshifting / lipid binding / 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 / 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
INHIBITOR VAL-SER-GLN-ASN-LEU-PSI(CH(OH)-CH2)-VAL-ILE-VAL (U-85548E) / Gag-Pol polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / Resolution: 2.5 Å
AuthorsJaskolski, M. / Miller, M. / Tomasselli, A.G. / Sawyer, T.K. / Staples, D.G. / Heinrikson, R.L. / Schneider, J. / Kent, S.B.H. / Wlodawer, A.
Citation
Journal: Biochemistry / Year: 1991
Title: Structure at 2.5-A resolution of chemically synthesized human immunodeficiency virus type 1 protease complexed with a hydroxyethylene-based inhibitor.
Authors: Jaskolski, M. / Tomasselli, A.G. / Sawyer, T.K. / Staples, D.G. / Heinrikson, R.L. / Schneider, J. / Kent, S.B. / Wlodawer, A.
#1: Journal: Science / Year: 1989
Title: Conserved Folding in Retroviral Proteases. Crystal Structure of a Synthetic HIV-1 Protease
Authors: Wlodawer, A. / Miller, M. / Jaskolski, M. / Sathyanarayana, B.K. / Baldwin, E. / Weber, I.T. / Selk, L.M. / Clawson, L. / Schneider, J. / Kent, S.B.H.
#2: Journal: Science / Year: 1989
Title: Molecular Modeling of the HIV-1 Protease and its Substrate Binding Site
Authors: Weber, I.T. / Miller, M. / Jaskolski, M. / Leis, J. / Skalka, A.M. / Wlodawer, A.
#3: Journal: Nature / Year: 1989
Title: Crystal Structure of a Retroviral Protease Proves Relationship to Aspartic Protease Family
Authors: Miller, M. / Jaskolski, M. / Rao, J.K.M. / Leis, J. / Wlodawer, A.
#4: Journal: Cell(Cambridge,Mass.) / Year: 1988
Title: Enzymatic Activity of a Synthetic 99 Residue Protein Corresponding to the Putative HIV-1 Protease
Authors: Schneider, J. / Kent, S.B.H.
History
DepositionOct 26, 1990Processing site: BNL
Revision 1.0Oct 31, 1993Provider: repository / Type: Initial release
Revision 1.1Mar 3, 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 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_validate_main_chain_plane / pdbx_validate_peptide_omega / pdbx_validate_rmsd_angle / struct_conn / struct_ref_seq_dif
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_validate_peptide_omega.auth_comp_id_1 / _pdbx_validate_peptide_omega.auth_comp_id_2 / _pdbx_validate_peptide_omega.auth_seq_id_1 / _pdbx_validate_peptide_omega.auth_seq_id_2 / _pdbx_validate_peptide_omega.omega / _pdbx_validate_rmsd_angle.angle_deviation / _pdbx_validate_rmsd_angle.angle_standard_deviation / _pdbx_validate_rmsd_angle.angle_target_value / _pdbx_validate_rmsd_angle.angle_value / _pdbx_validate_rmsd_angle.auth_atom_id_1 / _pdbx_validate_rmsd_angle.auth_atom_id_2 / _pdbx_validate_rmsd_angle.auth_atom_id_3 / _pdbx_validate_rmsd_angle.auth_comp_id_1 / _pdbx_validate_rmsd_angle.auth_comp_id_3 / _pdbx_validate_rmsd_angle.auth_seq_id_1 / _pdbx_validate_rmsd_angle.auth_seq_id_3 / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Remark 700SHEET THE DIMER INTERFACE IS COMPOSED OF INTERDIGITATED N- AND C-TERMINI FROM BOTH SUBUNITS FORMING ...SHEET THE DIMER INTERFACE IS COMPOSED OF INTERDIGITATED N- AND C-TERMINI FROM BOTH SUBUNITS FORMING A FOUR-STRANDED ANTIPARALLEL BETA-SHEET.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HIV-1 PROTEASE
B: HIV-1 PROTEASE
I: INHIBITOR VAL-SER-GLN-ASN-LEU-PSI(CH(OH)-CH2)-VAL-ILE-VAL (U-85548E)


Theoretical massNumber of molelcules
Total (without water)22,4013
Polymers22,4013
Non-polymers00
Water1,44180
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5250 Å2
ΔGint-31 kcal/mol
Surface area9400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.650, 58.760, 61.620
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Atom site foot note1: THE INHIBITOR RESIDUE LOV I 5 IS LEU-VAL WITH THE PEPTIDE BOND REPLACED BY CHOH-CH2.

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Components

#1: Protein HIV-1 PROTEASE


Mass: 10764.636 Da / Num. of mol.: 2
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: P03369
#2: Protein/peptide INHIBITOR VAL-SER-GLN-ASN-LEU-PSI(CH(OH)-CH2)-VAL-ILE-VAL (U-85548E)


Type: Peptide-like / Class: Inhibitor / Mass: 872.061 Da / Num. of mol.: 1 / Source method: obtained synthetically
References: INHIBITOR VAL-SER-GLN-ASN-LEU-PSI(CH(OH)-CH2)-VAL-ILE-VAL (U-85548E)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 80 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsTHE PEPTIDE BOND BETWEEN RESIDUES LEU I 5 AND VAL I 6 HAS BEEN REPLACED BY A HYDROXYETHYLENE GROUP ...THE PEPTIDE BOND BETWEEN RESIDUES LEU I 5 AND VAL I 6 HAS BEEN REPLACED BY A HYDROXYETHYLENE GROUP CH(OH)-CH2. THESE RESIDUES HAVE BEEN RENAMED AS LOV I 5 TO DENOTE THIS MODIFICATION.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.09 Å3/Da / Density % sol: 41.03 %
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop / Details: referred to Science 246.1149-1152 1989
Components of the solutions
*PLUS
Conc.: 60 % / Common name: ammonium sulfate

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2.5 Å / Num. all: 25199 / Num. obs: 6304

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Processing

SoftwareName: PROFFT / Classification: refinement
RefinementResolution: 2.5→10 Å /
RfactorNum. reflection
obs0.138 4768
Refinement stepCycle: LAST / Resolution: 2.5→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1577 0 0 80 1657
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0140.018
X-RAY DIFFRACTIONp_angle_d0.0530.035
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0670.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it2.4493
X-RAY DIFFRACTIONp_mcangle_it3.5773.5
X-RAY DIFFRACTIONp_scbond_it6.2395
X-RAY DIFFRACTIONp_scangle_it8.6338
X-RAY DIFFRACTIONp_plane_restr0.020.025
X-RAY DIFFRACTIONp_chiral_restr0.1790.15
X-RAY DIFFRACTIONp_singtor_nbd0.2170.3
X-RAY DIFFRACTIONp_multtor_nbd0.2640.3
X-RAY DIFFRACTIONp_xhyhbond_nbd0.3060.3
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor3.74
X-RAY DIFFRACTIONp_staggered_tor2010
X-RAY DIFFRACTIONp_orthonormal_tor18.220
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Refinement
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 10 Å / Num. reflection obs: 4768 / Rfactor obs: 0.138
Solvent computation
*PLUS
Displacement parameters
*PLUS

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