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- PDB-1a8g: HIV-1 PROTEASE IN COMPLEX WITH SDZ283-910 -

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Basic information

Entry
Database: PDB / ID: 1a8g
TitleHIV-1 PROTEASE IN COMPLEX WITH SDZ283-910
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 / 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 / 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 / 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 / Reverse transcriptase domain / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase (RT) catalytic domain profile. / Retrovirus capsid, C-terminal / 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
INHIBITOR SDZ283-910 / Chem-2Z4 / : / Gag-Pol polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / DIFFERENCE FOURIER / Resolution: 2.5 Å
AuthorsKallen, J. / Billich, A. / Scholz, D. / Auer, M. / Kungl, A.
CitationJournal: J.Mol.Biol. / Year: 1999
Title: X-ray structure and conformational dynamics of the HIV-1 protease in complex with the inhibitor SDZ283-910: agreement of time-resolved spectroscopy and molecular dynamics simulations.
Authors: Ringhofer, S. / Kallen, J. / Dutzler, R. / Billich, A. / Visser, A.J. / Scholz, D. / Steinhauser, O. / Schreiber, H. / Auer, M. / Kungl, A.J.
History
DepositionMar 24, 1998Processing site: BNL
Revision 1.0Jul 15, 1998Provider: 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 1.4Apr 18, 2018Group: Data collection / Other / Category: diffrn_detector / pdbx_database_status
Item: _diffrn_detector.detector / _pdbx_database_status.process_site
Revision 1.5Aug 2, 2023Group: Database references / Derived calculations / Refinement description
Category: database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.6May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,4883
Polymers21,6622
Non-polymers8261
Water1,24369
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5650 Å2
ΔGint-28 kcal/mol
Surface area9230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.100, 63.100, 83.600
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.503232, -0.864148, -0.002343), (-0.864148, 0.503236, 0.00168), (-0.002631, 0.001179, -0.999996)
Vector: -0.1634, -0.0318, 55.4793)

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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 / Plasmid: PTZPRT / Production host: Escherichia coli (E. coli) / Strain (production host): JM 105
References: GenBank: 9939861, UniProt: P03367*PLUS, HIV-1 retropepsin
#2: Chemical ChemComp-2Z4 / benzyl [(1R)-1-({(1S,2S,3S)-1-benzyl-2-hydroxy-4-({(1S)-1-[(2-hydroxy-4-methoxybenzyl)carbamoyl]-2-methylpropyl}amino)-3-[(4-methoxybenzyl)amino]-4-oxobutyl}carbamoyl)-2,2-dimethylpropyl]carbamate / SDZ283-910


Type: peptide-like, Peptide-like / Class: Inhibitor / Mass: 825.989 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C46H59N5O9 / References: INHIBITOR SDZ283-910
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 69 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.4 Å3/Da / Density % sol: 49 %
Crystal growpH: 7 / Details: pH 7.0
Crystal
*PLUS
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
25-25 %(v/v)ammonium sulfate1drop0.006mM
1inhibitor1drop0.006mM

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR571 / Wavelength: 1.5418
DetectorType: ENRAF-NONIUS FAST / Detector: DIFFRACTOMETER / Date: Sep 1, 1993
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→15 Å / Num. obs: 5696 / % possible obs: 81 % / Observed criterion σ(I): 3 / Redundancy: 4 % / Biso Wilson estimate: 39.4 Å2 / Rsym value: 0.087 / Net I/σ(I): 12
Reflection shellResolution: 2.5→2.67 Å / Redundancy: 4.1 % / Mean I/σ(I) obs: 3 / Rsym value: 0.27 / % possible all: 77
Reflection
*PLUS
Num. measured all: 22790 / Rmerge(I) obs: 0.087
Reflection shell
*PLUS
% possible obs: 77 % / Rmerge(I) obs: 0.27

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
MADNESdata reduction
PROCORdata scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: DIFFERENCE FOURIER
Starting model: PDB ENTRY 9HVP

9hvp


Resolution: 2.5→8 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 100000000 / Data cutoff low absF: 0.0001 / Isotropic thermal model: RESTRAINED / Cross valid method: A POSTERIORI / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.244 598 10.7 %RANDOM
Rwork0.15 ---
obs0.15 5566 87.4 %-
Displacement parametersBiso mean: 22.8 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.33 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.44 Å0.27 Å
Refinement stepCycle: LAST / Resolution: 2.5→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1520 0 60 69 1649
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.016
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_deg3.5
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d28.2
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.4
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it3.011.5
X-RAY DIFFRACTIONx_mcangle_it4.532
X-RAY DIFFRACTIONx_scbond_it4.92
X-RAY DIFFRACTIONx_scangle_it7.312.5
LS refinement shellResolution: 2.5→2.65 Å / Rfactor Rfree error: 0.033 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.322 93 11 %
Rwork0.218 752 -
obs--80.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARAM19X.PROTOPH19X.PRO
X-RAY DIFFRACTION2PARAM19.SOLTOPH19.PEP
X-RAY DIFFRACTION3PARAM19X.ITOPH19.PEPI
X-RAY DIFFRACTION4TOPH19X.I
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.15 / Rfactor Rwork: 0.15
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg28.2
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.4

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