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- PDB-4hvp: Structure of complex of synthetic HIV-1 protease with a substrate... -

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Basic information

Entry
Database: PDB / ID: 4hvp
TitleStructure of complex of synthetic HIV-1 protease with a substrate-based inhibitor at 2.3 Angstroms resolution
ComponentsHIV-1 PROTEASE
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 / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / RNA stem-loop binding ...HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / RNA stem-loop binding / viral penetration into host nucleus / host multivesicular body / 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 / 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-{(2S)-2-[(N-acetyl-L-threonyl-L-isoleucyl)amino]hexyl}-L-norleucyl-L-glutaminyl-N~5~-[amino(iminio)methyl]-L-ornithinamide / Chem-2NC / Gag-Pol polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / Resolution: 2.3 Å
AuthorsMiller, M. / Schneider, J. / Sathyanarayana, B.K. / Toth, M.V. / Marshall, G.R. / Clawson, L. / Selk, L. / Kent, S.B.H. / Wlodawer, A.
Citation
Journal: Science / Year: 1989
Title: Structure of complex of synthetic HIV-1 protease with a substrate-based inhibitor at 2.3 A resolution.
Authors: Miller, M. / Schneider, J. / Sathyanarayana, B.K. / Toth, M.V. / Marshall, G.R. / Clawson, L. / Selk, L. / 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
DepositionAug 8, 1989Processing site: BNL
Revision 1.0Apr 15, 1990Provider: 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 1.3Feb 27, 2013Group: Other
Revision 1.4Apr 3, 2013Group: Structure summary
Revision 1.5Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.6Mar 26, 2025Group: 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 / 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 / _pdbx_entry_details.has_protein_modification / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700THE DIMER INTERFACE IS COMPOSED OF INTERDIGITATED N- AND C-TERMINI FROM BOTH SUBUNITS FORMING A ...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

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Assembly

Deposited unit
A: HIV-1 PROTEASE
B: HIV-1 PROTEASE
B: N-{(2S)-2-[(N-acetyl-L-threonyl-L-isoleucyl)amino]hexyl}-L-norleucyl-L-glutaminyl-N~5~-[amino(iminio)methyl]-L-ornithinamide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,3003
Polymers21,5292
Non-polymers7711
Water1,26170
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5670 Å2
ΔGint-29 kcal/mol
Surface area8920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.700, 59.200, 62.450
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Atom site foot note1: THE PEPTIDE BOND BETWEEN RESIDUES NLE I 3 AND NLE I 4 HAS BEEN REDUCED AND IS -CH2-NH-.

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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: Chemical ChemComp-2NC / N-{(2S)-2-[(N-acetyl-L-threonyl-L-isoleucyl)amino]hexyl}-L-norleucyl-L-glutaminyl-N~5~-[amino(iminio)methyl]-L-ornithinamide / p2/NC


Type: peptide-like, Peptide-like / Class: Inhibitor / Mass: 770.983 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C35H68N11O8
References: N-{(2S)-2-[(N-acetyl-L-threonyl-L-isoleucyl)amino]hexyl}-L-norleucyl-L-glutaminyl-N~5~-[amino(iminio)methyl]-L-ornithinamide
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 70 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Nonpolymer detailsTHE PEPTIDE BOND BETWEEN SUBCOMPONENTS THE 2 NLE RESIDUES HAS BEEN REDUCED (IT IS -CH2-NH-)

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.14 Å3/Da / Density % sol: 42.57 %
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop / pH: 5.4
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
160 %sodium acetate1drop
220mM ammonium sulfate1reservior

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2.25 Å / Num. all: 8740 / Num. obs: 7943 / Observed criterion σ(I): 1.5 / Num. measured all: 55569 / Rmerge(I) obs: 0.068

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementResolution: 2.3→10 Å /
RfactorNum. reflection
obs0.176 7813
Refinement stepCycle: LAST / Resolution: 2.3→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1516 0 54 70 1640
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0190.02
X-RAY DIFFRACTIONp_angle_d0.0670.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0680.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.0021.5
X-RAY DIFFRACTIONp_mcangle_it1.592
X-RAY DIFFRACTIONp_scbond_it3.1113
X-RAY DIFFRACTIONp_scangle_it4.1644
X-RAY DIFFRACTIONp_plane_restr0.0140.02
X-RAY DIFFRACTIONp_chiral_restr0.220.15
X-RAY DIFFRACTIONp_singtor_nbd0.2710.3
X-RAY DIFFRACTIONp_multtor_nbd0.2970.3
X-RAY DIFFRACTIONp_xhyhbond_nbd0.2040.3
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor2.63
X-RAY DIFFRACTIONp_staggered_tor21.610
X-RAY DIFFRACTIONp_orthonormal_tor9.420
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: 'X-PLOR, PROLSQ' / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.176 / Highest resolution: 2.25 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS

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