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- PDB-1g35: CRYSTAL STRUCTURE OF HIV-1 PROTEASE IN COMPLEX WITH INHIBITOR, AHA024 -

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Basic information

Entry
Database: PDB / ID: 1g35
TitleCRYSTAL STRUCTURE OF HIV-1 PROTEASE IN COMPLEX WITH INHIBITOR, AHA024
ComponentsHIV-1 PROTEASE
KeywordsHYDROLASE / Protein-inhibitor complex
Function / homology
Function and homology information


RNA-directed DNA polymerase activity / 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 ...RNA-directed DNA polymerase activity / 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 / telomerase activity / viral penetration into host nucleus / RNA stem-loop binding / 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 / symbiont entry into host cell / viral translational frameshifting / lipid binding / 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
Chem-AHF / Gag-Pol polyprotein / Gag-Pol polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsLindberg, J. / Unge, T.
CitationJournal: J.Med.Chem. / Year: 2001
Title: Synthesis and comparative molecular field analysis (CoMFA) of symmetric and nonsymmetric cyclic sulfamide HIV-1 protease inhibitors.
Authors: Schaal, W. / Karlsson, A. / Ahlsen, G. / Lindberg, J. / Andersson, H.O. / Danielson, U.H. / Classon, B. / Unge, T. / Samuelsson, B. / Hulten, J. / Hallberg, A. / Karlen, A.
History
DepositionOct 23, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 6, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 7, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Aug 9, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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

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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)22,2723
Polymers21,6082
Non-polymers6651
Water2,576143
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5170 Å2
ΔGint-34 kcal/mol
Surface area9360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.500, 86.900, 46.900
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: 10803.756 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Genus: Lentivirus / Strain: BH7 / Production host: Escherichia coli (E. coli)
References: UniProt: P03368, UniProt: P03366*PLUS, HIV-1 retropepsin
#2: Chemical ChemComp-AHF / 2-[4-(HYDROXY-METHOXY-METHYL)-BENZYL]-7-(4-HYDROXYMETHYL-BENZYL)-1,1-DIOXO-3,6-BIS-PHENOXYMETHYL-1LAMBDA6-[1,2,7]THIADIAZEPANE-4,5-DIOL


Mass: 664.765 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C35H40N2O9S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 143 / 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: 8

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Sample preparation

CrystalDensity Matthews: 2.76 Å3/Da / Density % sol: 55.39 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 50 mM MES, 0.4 M NaCl, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Method: unknown

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Data collection

DiffractionMean temperature: 278 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 1.375 Å
DetectorType: MARRESEARCH / Detector: AREA DETECTOR / Date: Apr 3, 1998 / Details: mirrors
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.375 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. all: 22833 / Num. obs: 19437 / % possible obs: 85.1 % / Redundancy: 15.3 % / Rmerge(I) obs: 0.096 / Net I/σ(I): 7.7
Reflection shellResolution: 1.8→25 Å / Redundancy: 1.16 % / Rmerge(I) obs: 0.31 / Num. unique all: 1795 / % possible all: 80.2

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Processing

Software
NameClassification
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ajx

1ajx


Resolution: 1.8→50 Å / Cross valid method: THROUGHOUT / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.23 978 -Random
Rwork0.1949 ---
all0.1991 22833 --
obs-19059 83.5 %-
Refinement stepCycle: LAST / Resolution: 1.8→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1516 0 47 143 1706
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.2005
X-RAY DIFFRACTIONc_bond_d0.0058
LS refinement shellResolution: 1.8→50 Å
RfactorNum. reflection% reflection
Rfree0.2307 978 -
Rwork0.1949 --
obs-19059 85 %
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 50 Å / % reflection Rfree: 0 % / Rfactor Rfree: 0.23
Solvent computation
*PLUS
Displacement parameters
*PLUS
LS refinement shell
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 50 Å / % reflection Rfree: 85 % / Rfactor obs: 0.1949

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