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- PDB-1ivp: THE CRYSTALLOGRAPHIC STRUCTURE OF THE PROTEASE FROM HUMAN IMMUNOD... -

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Basic information

Entry
Database: PDB / ID: 1ivp
TitleTHE CRYSTALLOGRAPHIC STRUCTURE OF THE PROTEASE FROM HUMAN IMMUNODEFICIENCY VIRUS TYPE 2 WITH TWO SYNTHETIC PEPTIDIC TRANSITION STATE ANALOG INHIBITORS
ComponentsHIV-2 PROTEASE
KeywordsHYDROLASE/HYDROLASE INHIBITOR / ACID PROTEINASE / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


HIV-2 retropepsin / 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 / symbiont-mediated suppression of host gene expression ...HIV-2 retropepsin / 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 / symbiont-mediated suppression of host gene expression / viral penetration into host nucleus / RNA stem-loop binding / 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 / 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
gag protein p24 N-terminal 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 ...gag protein p24 N-terminal 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 / RNase H type-1 domain profile. / Ribonuclease H domain / Matrix protein, lentiviral and alpha-retroviral, N-terminal / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / Reverse transcriptase domain / Reverse transcriptase (RT) catalytic domain profile. / Retropepsins / Retroviral aspartyl protease / Aspartyl protease, retroviral-type family profile. / Peptidase A2A, retrovirus, catalytic / Reverse transcriptase (RNA-dependent DNA polymerase) / Retroviral matrix protein / Retrovirus capsid, C-terminal / Retrovirus capsid, N-terminal / zinc finger / Zinc knuckle / Zinc finger, CCHC-type superfamily / Cathepsin D, subunit A; domain 1 / Acid Proteases / Zinc finger, CCHC-type / Zinc finger CCHC-type profile. / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Ribonuclease H superfamily / Aspartic peptidase domain superfamily / Ribonuclease H-like superfamily / Reverse transcriptase/Diguanylate cyclase domain / DNA/RNA polymerase superfamily / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Noa-His-Cha.psi.[CHOHCHOH]Val-Ile-Amp, U75875 / Chem-1ZK / Gag-Pol polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus 2
MethodX-RAY DIFFRACTION / Resolution: 2.5 Å
AuthorsMulichak, A.M. / Watenpaugh, K.D.
CitationJournal: J.Biol.Chem. / Year: 1993
Title: The crystallographic structure of the protease from human immunodeficiency virus type 2 with two synthetic peptidic transition state analog inhibitors.
Authors: Mulichak, A.M. / Hui, J.O. / Tomasselli, A.G. / Heinrikson, R.L. / Curry, K.A. / Tomich, C.S. / Thaisrivongs, S. / Sawyer, T.K. / Watenpaugh, K.D.
History
DepositionMar 18, 1993Processing site: BNL
Revision 1.0Jul 15, 1993Provider: repository / Type: Initial release
Revision 1.1Mar 24, 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 1.5Feb 7, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly / struct_ref_seq_dif / struct_site
Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_ref_seq_dif.details / _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-2 PROTEASE
B: HIV-2 PROTEASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,2383
Polymers21,4252
Non-polymers8131
Water73941
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5290 Å2
ΔGint-23 kcal/mol
Surface area9300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)33.190, 44.950, 135.650
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Atom site foot note1: SEE REMARK 5 ABOVE. / 2: SEE REMARK 6 ABOVE.
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.2141, 0.9365, -0.2776), (0.9365, -0.2776, -0.2141), (-0.2776, -0.2131, -0.9365)
Vector: -10.0269, 26.1547, 44.3882)
DetailsTHE NON-CRYSTALLOGRAPHIC C(2) SYMMETRY RELATING THE TWO MONOMERS OF THE PROTEASE DIMER IS GIVEN ON THE MTRIX RECORDS BELOW. THIS TRANSFORMATION WILL YIELD APPROXIMATE COORDINATES FOR CHAIN B WHEN APPLIED TO CHAIN A.

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Components

#1: Protein HIV-2 PROTEASE


Mass: 10712.315 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 2 / Genus: Lentivirus / Production host: Escherichia coli (E. coli) / References: UniProt: P04584
#2: Chemical ChemComp-1ZK / 4-[(2R)-3-{[(1S,2S,3R,4S)-1-(cyclohexylmethyl)-2,3-dihydroxy-5-methyl-4-({(1S,2R)-2-methyl-1-[(pyridin-2-ylmethyl)carba moyl]butyl}carbamoyl)hexyl]amino}-2-{[(naphthalen-1-yloxy)acetyl]amino}-3-oxopropyl]-1H-imidazol-3-ium / U75875


Type: peptide-like, Peptide-like / Class: Inhibitor / Mass: 813.016 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C45H62N7O7 / References: Noa-His-Cha.psi.[CHOHCHOH]Val-Ile-Amp, U75875
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 41 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsCOMPONENT CAV 3 OF THE INHIBITOR 1ZK B 100 IS THE DIPEPTIDE ISOSTERE CYCLOHEXYL ALANINE PSI(CHOH- ...COMPONENT CAV 3 OF THE INHIBITOR 1ZK B 100 IS THE DIPEPTIDE ISOSTERE CYCLOHEXYL ALANINE PSI(CHOH-CHOH)VALINE. THE VALINE HAS A C-OH GROUP IN PLACE OF THE USUAL MAIN CHAIN N ATOM. COMPONENT APY 5 WAS IDENTIFIED AS AMP IN THE PAPER CITED ON THE JRNL RECORDS ABOVE.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.27 Å3/Da / Density % sol: 45.91 %
Crystal grow
*PLUS
pH: 7 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
16 mg/mlenzyme1drop
20.1 MMOPS1drop
310 %glycerol1drop
45 %ethylene glycol1drop
525-30 %PEG40001reservoir
60.1 MHEPES1reservoir
73-4 %1-butanol1reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2.5 Å / Num. obs: 5285 / % possible obs: 86 % / Rmerge F obs: 0.095 / Num. measured all: 20722

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementRfactor obs: 0.197 / Highest resolution: 2.5 Å
Refinement stepCycle: LAST / Highest resolution: 2.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1479 0 59 41 1579
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.015
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d
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_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Refinement
*PLUS
Highest resolution: 2.5 Å / Num. reflection obs: 5563 / Rfactor obs: 0.197
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 18 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal targetDev ideal
X-RAY DIFFRACTIONp_bond_d0.02
X-RAY DIFFRACTIONp_angle_deg0.0350.043
X-RAY DIFFRACTIONp_planar_d0.050.046
X-RAY DIFFRACTIONp_plane_restr0.020.012
X-RAY DIFFRACTIONp_chiral_restr0.20.2
X-RAY DIFFRACTIONp_mcbond_it1.50.73
X-RAY DIFFRACTIONp_scbond_it1.50.69
X-RAY DIFFRACTIONp_mcangle_it1.51.18
X-RAY DIFFRACTIONp_scangle_it1.51.02

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