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- PDB-1hvc: CRYSTAL STRUCTURE OF A TETHERED DIMER OF HIV-1 PROTEASE COMPLEXED... -

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Basic information

Entry
Database: PDB / ID: 1hvc
TitleCRYSTAL STRUCTURE OF A TETHERED DIMER OF HIV-1 PROTEASE COMPLEXED WITH AN INHIBITOR
ComponentsHIV-1 PROTEASE
KeywordsHYDROLASE(ACID PROTEASE)
Function / homology
Function and homology information


host multivesicular body / viral genome integration into host DNA / establishment of integrated proviral latency / RNA-directed DNA polymerase activity / endonuclease activity / aspartic-type endopeptidase activity / virion membrane / proteolysis / DNA binding / zinc ion binding
Similarity search - Function
: / Retropepsin-like catalytic 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. / Cathepsin D, subunit A; domain 1 ...: / Retropepsin-like catalytic 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. / Cathepsin D, subunit A; domain 1 / Acid Proteases / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Aspartic peptidase domain superfamily / Reverse transcriptase/Diguanylate cyclase domain / DNA/RNA polymerase superfamily / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Chem-A79 / Protease / Pol protein
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / Resolution: 1.8 Å
AuthorsBhat, T.N. / Baldwin, E.T. / Erickson, J.W.
Citation
Journal: Nat.Struct.Biol. / Year: 1994
Title: Crystal structure of a tethered dimer of HIV-1 proteinase complexed with an inhibitor.
Authors: Bhat, T.N. / Baldwin, E.T. / Liu, B. / Cheng, Y.S. / Erickson, J.W.
#1: Journal: J.Am.Chem.Soc. / Year: 1994
Title: Influence of Stereochemistry on Activity and Binding Modes for C2 Symmetry-Based Diol Inhibitors of HIV-1 Protease
Authors: Hosur, M.V. / Bhat, T.N. / Kempf, D.J. / Baldwin, E.T. / Liu, B. / Gulnik, S. / Wideburg, N.E. / Norbeck, D.W. / Appelt, K. / Erickson, J.W.
#2: Journal: Annu.Rev.Biochem. / Year: 1993
Title: Structure-Based Inhibitors of HIV-1 Protease
Authors: Wlodawer, A. / Erickson, J.W.
History
DepositionJun 22, 1994Processing site: BNL
Revision 1.0Oct 15, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 10, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 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_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_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

Downloads & links

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Assembly

Deposited unit
A: HIV-1 PROTEASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,7572
Polymers21,9621
Non-polymers7951
Water1,22568
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.100, 59.800, 62.200
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Atom site foot note1: ILE 15B - GLY 16B OMEGA = 216.69 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
2: SER 203 - GLY 204 OMEGA = 0.34 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
3: ILE 15A - GLY 16A OMEGA = 210.89 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
4: GLY 16A - GLY 17A OMEGA = 348.40 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION

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Components

#1: Protein HIV-1 PROTEASE


Mass: 21961.850 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Genus: Lentivirus / Gene: SYNTHETIC GENE / Production host: Escherichia coli (E. coli) / References: UniProt: O92139, UniProt: Q4VE97*PLUS
#2: Chemical ChemComp-A79 / N-{1-BENZYL-(2S,3S)-2,3-DIHYDROXY-4-[3-METHYL-2-(3-METHYL-3-PYRIDIN-2-YLMETHYL-UREIDO)-BUTYRYLAMINO]-5-PHENYL-PENTYL}-3-METHYL-2-(3-METHYL-3-PYRIDIN-2-YLMETHYL-UREIDO)-BUTYRAMIDE


Mass: 794.981 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C44H58N8O6
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 68 / 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: 2.2 Å3/Da / Density % sol: 44.21 %
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop / Details: using macroseeding
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
16 mg/mlHIV PR1drop
350 mMsodium acetate1drop
410 mMDTT1drop
510 %DMSO1drop
666 mMsodium citrate1drop
7132 mM1dropNaPO4
834 %satammonium sulfate1drop
966 mMsodium citrate1reservoir
2A-769281drop
10132 mM1reservoirNaPO4
1134 %satammonium sulfate1reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 10 Å / Num. obs: 16421 / % possible obs: 88 % / Num. measured all: 39662 / Rmerge(I) obs: 0.064

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 1.8→10 Å /
Num. reflection% reflection
obs16421 88 %
Refinement stepCycle: LAST / Resolution: 1.8→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3171 0 116 204 3491
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.018
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg3
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.2
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_d / Dev ideal: 3

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