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- PDB-2fgu: X-ray crystal structure of HIV-1 Protease T80S variant in complex... -

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Basic information

Entry
Database: PDB / ID: 2fgu
TitleX-ray crystal structure of HIV-1 Protease T80S variant in complex with the inhibitor saquinavir used to explore the role of invariant Thr80 in HIV-1 protease structure, function, and viral infectivity.
ComponentsProtease
KeywordsHYDROLASE / HIV Protease / drug resistance / enzyme kinetics / sequence conservation / protein structure
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 / symbiont-mediated suppression of host gene expression / 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
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 / Reverse transcriptase domain / Reverse transcriptase (RNA-dependent DNA polymerase) / 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 / Cathepsin D, subunit A; domain 1 / Acid Proteases / 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
ASPARAGINE / 2-METHYL-DECAHYDRO-ISOQUINOLINE-3-CARBOXYLIC ACID / (2S)-2-amino-3-phenylpropane-1,1-diol / TERTIARY-BUTYLAMINE / PHOSPHATE ION / quinoline-2-carboxylic acid / Protease / Gag-Pol polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsFoulkes, J.E. / Prabu-Jeyabalan, M. / Cooper, D. / Schiffer, C.A.
CitationJournal: J.Virol. / Year: 2006
Title: Role of invariant Thr80 in human immunodeficiency virus type 1 protease structure, function, and viral infectivity.
Authors: Foulkes, J.E. / Prabu-Jeyabalan, M. / Cooper, D. / Henderson, G.J. / Harris, J. / Swanstrom, R. / Schiffer, C.A.
History
DepositionDec 22, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 7, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Revision 1.4Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Remark 600HETEROGEN THE ENTIRE CHAIN I IS AN INHIBITOR SAQUINAVIR.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protease
B: Protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,79312
Polymers21,5752
Non-polymers1,21810
Water2,342130
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6120 Å2
ΔGint-36 kcal/mol
Surface area9030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.50, 57.93, 61.62
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe entire HIV-1 protease dimer in complex with the inhibitor saquinavir.

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Protease / Retropepsin / PR


Mass: 10787.736 Da / Num. of mol.: 2 / Mutation: Q7K, I64V, T80S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Genus: Lentivirus / Strain: SF2 / Gene: GAG / Plasmid: pXC35 / Production host: Escherichia coli (E. coli) / Strain (production host): TAP106
References: UniProt: O38716, UniProt: P03369*PLUS, HIV-1 retropepsin

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Non-polymers , 7 types, 140 molecules

#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-QNC / quinoline-2-carboxylic acid


Mass: 173.168 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H7NO2
#4: Chemical ChemComp-ASN / ASPARAGINE


Type: L-peptide linking / Mass: 132.118 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H8N2O3
#5: Chemical ChemComp-HPH / (2S)-2-amino-3-phenylpropane-1,1-diol / (2S)-2-amino-3-phenylpropane-1,1-diol


Type: peptide-like / Mass: 167.205 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H13NO2
#6: Chemical ChemComp-DIQ / 2-METHYL-DECAHYDRO-ISOQUINOLINE-3-CARBOXYLIC ACID


Mass: 197.274 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H19NO2
#7: Chemical ChemComp-NTB / TERTIARY-BUTYLAMINE


Mass: 73.137 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H11N
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 130 / 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: 2.09 Å3/Da / Density % sol: 41.08 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.126 M Sodium Phosphate pH 6.2, 0.063 M Sodium Citrate, 23-24% Ammonium Sulfate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Nov 5, 2004 / Details: Osmic Mirrors
RadiationMonochromator: Osmic Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→42.22 Å / Num. all: 12625 / Num. obs: 12625 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7 % / Rmerge(I) obs: 0.073 / Rsym value: 0.073 / Net I/σ(I): 8.2

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1F7A

1f7a


Resolution: 2→42.22 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.93 / SU B: 4.559 / SU ML: 0.127 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.205 / ESU R Free: 0.178 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23235 612 4.9 %RANDOM
Rwork0.1764 ---
all0.1791 12625 --
obs0.17911 11977 99.09 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 21.948 Å2
Baniso -1Baniso -2Baniso -3
1--0.73 Å20 Å20 Å2
2--0.52 Å20 Å2
3---0.21 Å2
Refinement stepCycle: LAST / Resolution: 2→42.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1462 0 74 130 1666
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0221589
X-RAY DIFFRACTIONr_bond_other_d00.021518
X-RAY DIFFRACTIONr_angle_refined_deg1.6132.0272178
X-RAY DIFFRACTIONr_angle_other_deg0.67933519
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9425200
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.2072550
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.64415245
X-RAY DIFFRACTIONr_dihedral_angle_4_deg27.859156
X-RAY DIFFRACTIONr_chiral_restr0.0930.2256
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021719
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02285
X-RAY DIFFRACTIONr_nbd_refined0.1990.3231
X-RAY DIFFRACTIONr_nbd_other0.2130.31461
X-RAY DIFFRACTIONr_nbtor_refined0.1760.5757
X-RAY DIFFRACTIONr_nbtor_other0.0920.5954
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.190.5153
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0730.51
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0620.311
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1770.377
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2160.522
X-RAY DIFFRACTIONr_mcbond_it1.21.51259
X-RAY DIFFRACTIONr_mcbond_other0.2631.5416
X-RAY DIFFRACTIONr_mcangle_it1.44321601
X-RAY DIFFRACTIONr_scbond_it2.2173711
X-RAY DIFFRACTIONr_scangle_it3.3214.5577
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.331 47 -
Rwork0.235 783 -
obs--90.91 %

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