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- PDB-5hvp: CRYSTALLOGRAPHIC ANALYSIS OF A COMPLEX BETWEEN HUMAN IMMUNODEFICI... -

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Basic information

Entry
Database: PDB / ID: 5hvp
TitleCRYSTALLOGRAPHIC ANALYSIS OF A COMPLEX BETWEEN HUMAN IMMUNODEFICIENCY VIRUS TYPE 1 PROTEASE AND ACETYL-PEPSTATIN AT 2.0-ANGSTROMS RESOLUTION
Components
  • ACETYL-*PEPSTATIN
  • HIV-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 / 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 / symbiont-mediated suppression of host gene expression / RNA stem-loop binding / RNA-directed DNA polymerase activity / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / host cell / viral nucleocapsid / endonuclease activity / DNA recombination / DNA-directed DNA polymerase / Hydrolases; Acting on ester bonds / aspartic-type endopeptidase activity / DNA-directed DNA polymerase activity / symbiont entry into host cell / viral translational frameshifting / lipid binding / host cell nucleus / host cell plasma membrane / structural molecule activity / virion membrane / 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 / Reverse transcriptase domain / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase (RT) catalytic domain profile. / Retropepsins / Retroviral aspartyl protease / Aspartyl protease, retroviral-type family profile. / Peptidase A2A, retrovirus, catalytic / Retrovirus capsid, C-terminal / Retroviral matrix protein / Retrovirus capsid, N-terminal / zinc finger / Zinc knuckle / Cathepsin D, subunit A; domain 1 / Acid Proteases / 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
ACETYL-PEPSTATIN / Gag-Pol polyprotein / Pol polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
Streptomyces (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2 Å
AuthorsFitzgerald, P.M.D. / Mckeever, B.M. / Vanmiddlesworth, J.F. / Springer, J.P.
Citation
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-A resolution.
Authors: Fitzgerald, P.M. / McKeever, B.M. / VanMiddlesworth, J.F. / Springer, J.P. / Heimbach, J.C. / Leu, C.T. / Herber, W.K. / Dixon, R.A. / Darke, P.L.
#1: 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.
#2: Journal: J.Biol.Chem. / Year: 1989
Title: Crystallization of the Aspartylprotease from the Human Immunodefeciency Virus, HIV-1
Authors: Mckeever, B.M. / Navia, M.A. / Fitzgerald, P.M.D. / Springer, J.P. / Leu, C.-T. / Heimbach, J.C. / Herber, W.K. / Sigal, I.S. / Darke, P.L.
#3: Journal: J.Biol.Chem. / Year: 1989
Title: Human Immunodeficiency Virus Protease. Bacterial Expression and Characterization of the Purified Aspartic Protease
Authors: Darke, P.L. / Leu, C.-T. / Davis, L.J. / Heimabch, J.C. / Diehl, R.E. / Hill, W.S. / Dixon, R.A.F. / Sigal, I.S.
History
DepositionApr 30, 1990Processing site: BNL
Revision 1.0Oct 15, 1991Provider: repository / Type: Initial release
Revision 1.1Mar 25, 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 1.4Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.5Nov 20, 2024Group: 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_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700SHEET THE SHEET *S1* IS FORMED BY THE INTERDIGITATING STRANDS FROM THE TWO MONOMERS OF THE DIMERIC ...SHEET THE SHEET *S1* IS FORMED BY THE INTERDIGITATING STRANDS FROM THE TWO MONOMERS OF THE DIMERIC ENZYME. STRANDS 1 AND 3 ARE FROM CHAIN *A*. STRANDS 2 AND 4 ARE FROM CHAIN *B*.

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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
C: ACETYL-*PEPSTATIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,3605
Polymers22,2893
Non-polymers712
Water3,063170
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5570 Å2
ΔGint-48 kcal/mol
Surface area8920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.390, 86.700, 46.270
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Atom site foot note1: SIDE CHAINS OF THESE RESIDUES HAVE BEEN MODELED IN TWO ALTERNATE CONFORMATIONS AND ASSIGNED ALTERNATE LOCATION INDICATORS *1* AND *2*.
2: THE OCCUPANCIES OF SOLVENT MOLECULES WHICH CORRELATED WITH STATIC DISORDER IN THE PROTEIN HAVE BEEN SET TO LESS THAN UNITY. WATER MOLECULES WITH ALTERNATE LOCATION INDICATOR *1* AND OCCUPANCY 0.58 ...2: THE OCCUPANCIES OF SOLVENT MOLECULES WHICH CORRELATED WITH STATIC DISORDER IN THE PROTEIN HAVE BEEN SET TO LESS THAN UNITY. WATER MOLECULES WITH ALTERNATE LOCATION INDICATOR *1* AND OCCUPANCY 0.58 CORRELATE WITH INHIBITOR ORIENTATIO *1*. WATER MOLECULES WITH ALTERNATE LOCATION INDICATOR *2* AND OCCUPANCY 0.42 CORRELATE WITH INHIBITOR ORIENTATION *2* IF THE SOLVENT MOLECULE IS DISTANT FROM THE BOUND INHIBITOR AN OCCUPANCY OF 0.50 HAS BEEN ASSIGNED.

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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: Q9WFL7, UniProt: P12497*PLUS
#2: Protein/peptide ACETYL-*PEPSTATIN


Type: Oligopeptide / Class: Inhibitor / Mass: 627.812 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces (bacteria) / References: ACETYL-PEPSTATIN
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 170 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHE INHIBITOR BINDS TO THE ENZYME IN TWO ROUGHLY TWOFOLD SYMMETRIC ORIENTATIONS. THE ALTERNATE ...THE INHIBITOR BINDS TO THE ENZYME IN TWO ROUGHLY TWOFOLD SYMMETRIC ORIENTATIONS. THE ALTERNATE CONFORMATIONS ARE REPRESENTED BY THE ALTERNATE LOCATION INDICATORS *1* AND *2*. THE FIRST ORIENTATION, *1*, WAS DENOTED A IN THE PUBLICATION CITED IN THE *JRNL* RECORDS ABOVE, WHILE THE ALTERNATE ORIENTATION, *2*, WAS DENOTED B.
Has protein modificationY
Sequence detailsIN THE PAPER CITED IN THE *JRNL* RECORDS ABOVE, THE *B* CHAIN RESIDUES WERE NUMBERED FROM 201 TO ...IN THE PAPER CITED IN THE *JRNL* RECORDS ABOVE, THE *B* CHAIN RESIDUES WERE NUMBERED FROM 201 TO 299. THIS NUMBERING SCHEME HAS BEEN RETAINED.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.63 Å3/Da / Density % sol: 53.16 %
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

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 1.92 Å / Lowest resolution: 9999 Å / Num. obs: 13397 / % possible obs: 72.6 % / Observed criterion σ(I): 1 / Num. measured all: 36470 / Rmerge(I) obs: 0.0439

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementResolution: 2→8 Å / σ(I): 0 /
RfactorNum. reflection
obs0.176 12901
Refinement stepCycle: LAST / Resolution: 2→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1550 0 2 170 1722
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0180.02
X-RAY DIFFRACTIONp_angle_d0.0380.03
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0430.04
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_restr0.0150.02
X-RAY DIFFRACTIONp_chiral_restr0.1770.15
X-RAY DIFFRACTIONp_singtor_nbd0.2160.5
X-RAY DIFFRACTIONp_multtor_nbd0.2070.5
X-RAY DIFFRACTIONp_xhyhbond_nbd0.2450.5
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor2.63
X-RAY DIFFRACTIONp_staggered_tor17.415
X-RAY DIFFRACTIONp_orthonormal_tor18.120
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Refinement
*PLUS
Highest resolution: 2 Å / Lowest resolution: 8 Å / Num. reflection obs: 12901 / Rfactor obs: 0.176
Solvent computation
*PLUS
Displacement parameters
*PLUS

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