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- PDB-4phv: X-RAY CRYSTAL STRUCTURE OF THE HIV PROTEASE COMPLEX WITH L-700,41... -

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Basic information

Entry
Database: PDB / ID: 4phv
TitleX-RAY CRYSTAL STRUCTURE OF THE HIV PROTEASE COMPLEX WITH L-700,417, AN INHIBITOR WITH PSEUDO C2 SYMMETRY
ComponentsHIV-1 PROTEASE
KeywordsHYDROLASE(ASPARTIC PROTEINASE)
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 / host multivesicular body / 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 / 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
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
Chem-VAC / Gag-Pol polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / Resolution: 2.1 Å
AuthorsBone, R.
Citation
Journal: J.Am.Chem.Soc. / Year: 1991
Title: X-Ray Crystal Structure of the HIV Protease Complex with L-700,417, an Inhibitor with Pseudo C2 Symmetry
Authors: Bone, R. / Vacca, J.P. / Anderson, P.S. / Holloway, M.K.
#1: Journal: Science / Year: 1990
Title: Design, Activity, and 2.8 Angstroms Crystal Structure of a C2 Symmetric Inhibitor Complexed to HIV-1 Protease
Authors: Erickson, J. / Neidhart, D.J. / Van Drie, J. / Kempf, D.J. / Wang, X.C. / Norbeck, D.W. / Plattner, J.J. / Rittenhouse, J.W. / Turon, M. / Wideburg, N. / Kohlbrenner, W.E. / Simmer, R. / ...Authors: Erickson, J. / Neidhart, D.J. / Van Drie, J. / Kempf, D.J. / Wang, X.C. / Norbeck, D.W. / Plattner, J.J. / Rittenhouse, J.W. / Turon, M. / Wideburg, N. / Kohlbrenner, W.E. / Simmer, R. / Helfrich, R. / Paul, D.A. / Knigge, M.
#2: Journal: J.Biol.Chem. / Year: 1990
Title: Crystallographic Analysis of a Complex between Human Immunodeficiency Virus Type 1 Protease and Acetyl-Pepstatin at 2.0 Angstroms Resolution
Authors: Fitzgerald, P.M.D. / Mckeever, B.M. / Van Middlesworth, J.F. / Springer, J.P. / Heimbach, J.C. / Leu, C.-T. / Herber, W.K. / Dixon, R.A.F. / Darke, P.L.
#3: Journal: Proc.Natl.Acad.Sci.USA / Year: 1990
Title: X-Ray Crystallographic Structure of a Complex between a Synthetic Protease of Human Immunodeficiency Virus 1 and a Substrate-Based Hydroxyethylamine Inhibitor
Authors: Swain, A.L. / Miller, M.M. / Green, J. / Rich, D.H. / Schneider, J. / Kent, S.B.H. / Wlodawer, A.
#4: Journal: Nature / Year: 1989
Title: Three-Dimensional Structure of Aspartyl Protease from Human Immunodeficiency Virus HIV-1
Authors: Navia, M.A. / Fitzgerald, P.M.D. / Mckeever, B.M. / Leu, C.-T. / Heimbach, J.C. / Herber, W.K. / Sigal, I.S. / Darke, P.L. / Springer, J.P.
#5: 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. / Clawson, L. / Schneider, J. / Kent, S.B.H.
History
DepositionOct 4, 1991Processing site: BNL
Revision 1.0Oct 31, 1993Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 28, 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_conn / 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_conn.pdbx_leaving_atom_flag / _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

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Assembly

Deposited unit
A: HIV-1 PROTEASE
B: HIV-1 PROTEASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,8994
Polymers21,6622
Non-polymers1,2382
Water1,874104
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6080 Å2
ΔGint-43 kcal/mol
Surface area9070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.880, 86.800, 46.790
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein HIV-1 PROTEASE


Mass: 10830.781 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: P12497
#2: Chemical ChemComp-VAC / N,N-BIS(2-HYDROXY-1-INDANYL)-2,6- DIPHENYLMETHYL-4-HYDROXY-1,7-HEPTANDIAMIDE


Mass: 618.761 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C39H42N2O5
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 104 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.76 Å3/Da / Density % sol: 55.41 %
Crystal grow
*PLUS
pH: 5.4 / Method: vapor diffusion / Details: macro-seeding
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
1100 mMsodium acetate11
2400-800 mMsodium chloride11

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Data collection

Reflection
*PLUS
Highest resolution: 2.1 Å / % possible obs: 97.2 % / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.07

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementResolution: 2.1→8 Å / σ(F): 0 /
RfactorNum. reflection
obs0.18 12981
Refinement stepCycle: LAST / Resolution: 2.1→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1520 0 92 104 1716
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0150.02
X-RAY DIFFRACTIONp_angle_d0.0370.03
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0450.04
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it0.911
X-RAY DIFFRACTIONp_mcangle_it1.5761.5
X-RAY DIFFRACTIONp_scbond_it1.1981
X-RAY DIFFRACTIONp_scangle_it2.051.5
X-RAY DIFFRACTIONp_plane_restr0.0130.02
X-RAY DIFFRACTIONp_chiral_restr0.1580.15
X-RAY DIFFRACTIONp_singtor_nbd0.1940.5
X-RAY DIFFRACTIONp_multtor_nbd0.2060.5
X-RAY DIFFRACTIONp_xhyhbond_nbd0.2620.5
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor2.53
X-RAY DIFFRACTIONp_staggered_tor18.715
X-RAY DIFFRACTIONp_orthonormal_tor15.720
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: PROLSQ / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.1 Å / Lowest resolution: 8 Å / Num. reflection all: 12981 / σ(F): 0 / Rfactor all: 0.18
Solvent computation
*PLUS
Displacement parameters
*PLUS

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