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- PDB-4i8z: Crystal structure of wild type HIV-1 protease in complex with non... -

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Basic information

Entry
Database: PDB / ID: 4i8z
TitleCrystal structure of wild type HIV-1 protease in complex with non-peptidic inhibitor, GRL008
ComponentsProtease
KeywordsHYDROLASE/HYDROLASE INHIBITOR / HIV-1 protease / HIV-1 protease-inhibitor complex / hydrolase / GRL008 / non-peptidic inhibitor / protease inhibitor / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


HIV-1 retropepsin / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / host multivesicular body / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / viral penetration into host nucleus / establishment of integrated proviral latency ...HIV-1 retropepsin / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / host multivesicular body / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / viral penetration into host nucleus / establishment of integrated proviral latency / RNA stem-loop binding / RNA-directed DNA polymerase activity / host cell / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / symbiont-mediated suppression of host gene expression / 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 / 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. / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / Retropepsin-like catalytic domain / Matrix protein, lentiviral and alpha-retroviral, N-terminal / Ribonuclease H domain / RNase H type-1 domain profile. / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase domain / 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 / 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
Chem-G08 / Gag-Pol polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus type 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsYedidi, R.S. / Palmer, I. / Das, D. / Wingfield, P.T. / Ghosh, A.K. / Mitsuya, H.
CitationJournal: Antimicrob.Agents Chemother. / Year: 2013
Title: P2' benzene carboxylic acid moiety is associated with decrease in cellular uptake: evaluation of novel non-peptidic HIV-1 protease inhibitors containing P2 bis-tetrahydrofuran moiety.
Authors: Yedidi, R.S. / Maeda, K. / Fyvie, W.S. / Steffey, M. / Davis, D.A. / Palmer, I. / Aoki, M. / Kaufman, J.D. / Stahl, S.J. / Garimella, H. / Das, D. / Wingfield, P.T. / Ghosh, A.K. / Mitsuya, H.
History
DepositionDec 4, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 24, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 25, 2013Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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: Protease
B: Protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,1833
Polymers21,6082
Non-polymers5761
Water2,306128
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3950 Å2
ΔGint-23 kcal/mol
Surface area9400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.120, 62.120, 81.740
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Protein Protease


Mass: 10803.756 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus type 1 / Production host: Escherichia coli (E. coli) / References: UniProt: P0C6F2, HIV-1 retropepsin
#2: Chemical ChemComp-G08 / (3R,3aS,6aR)-hexahydrofuro[2,3-b]furan-3-yl [(2S,3R)-4-{[(4-carbamoylphenyl)sulfonyl](2-methylpropyl)amino}-3-hydroxy-1-phenylbutan-2-yl]carbamate


Mass: 575.674 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C28H37N3O8S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 128 / 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: 2.11 Å3/Da / Density % sol: 41.62 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 1.6 M ammonium sulfate (precipitant) in 0.1 M BICINE buffer, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 14, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.75→32.54 Å / Num. obs: 17977 / Rmerge(I) obs: 0.075

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.75→29.034 Å / SU ML: 0.25 / σ(F): 2.03 / Phase error: 22.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2202 915 5.09 %
Rwork0.18 --
obs0.182 17967 99.36 %
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 51.245 Å2 / ksol: 0.407 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.4446 Å2-0 Å2-0 Å2
2--0.4446 Å20 Å2
3----0.8892 Å2
Refinement stepCycle: LAST / Resolution: 1.75→29.034 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1516 0 40 128 1684
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0181628
X-RAY DIFFRACTIONf_angle_d1.9272212
X-RAY DIFFRACTIONf_dihedral_angle_d15.54638
X-RAY DIFFRACTIONf_chiral_restr0.144260
X-RAY DIFFRACTIONf_plane_restr0.01268
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7501-1.84240.30251200.24112417X-RAY DIFFRACTION99
1.8424-1.95780.24651350.21162427X-RAY DIFFRACTION99
1.9578-2.10890.23191210.19342439X-RAY DIFFRACTION99
2.1089-2.3210.20591320.19332429X-RAY DIFFRACTION100
2.321-2.65670.26461440.20512412X-RAY DIFFRACTION100
2.6567-3.34640.26071350.18812446X-RAY DIFFRACTION100
3.3464-29.03850.17271280.15232482X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: -22.7883 Å / Origin y: 0.0016 Å / Origin z: -0.2857 Å
111213212223313233
T0.1736 Å20.0001 Å2-0.0009 Å2-0.1062 Å20.0347 Å2--0.1543 Å2
L1.6989 °2-0.0092 °20.0121 °2-4.2663 °22.8507 °2--3.1816 °2
S-0.0007 Å °-0.0116 Å °0.0072 Å °0.0264 Å °0.1055 Å °-0.1838 Å °0.0293 Å °0.122 Å °-0.048 Å °
Refinement TLS groupSelection details: all

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