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- PDB-3tlh: STRUCTURAL STUDIES OF HIV AND FIV PROTEASES COMPLEXED WITHAN EFFI... -

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Basic information

Entry
Database: PDB / ID: 3tlh
TitleSTRUCTURAL STUDIES OF HIV AND FIV PROTEASES COMPLEXED WITHAN EFFICIENT INHIBITOR OF FIV PR
ComponentsPROTEIN (PROTEASE)
KeywordsHYDROLASE/HYDROLASE INHIBITOR / HIV PROTEASE / 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 / DNA integration / host multivesicular body / 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 / DNA integration / host multivesicular body / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / RNA stem-loop binding / viral penetration into host nucleus / 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 / Retrovirus capsid, C-terminal / Reverse transcriptase domain / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase (RT) catalytic domain profile. / 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
N-[(benzyloxy)carbonyl]-L-alanyl-N-[(1R)-1-benzyl-2-oxoethyl]-L-valinamide / Chem-3TL / Gag-Pol polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus type 1
MethodX-RAY DIFFRACTION / OTHER / Resolution: 2 Å
AuthorsLi, M. / Lee, T. / Morris, G. / Laco, G. / Wong, C. / Olson, A. / Elder, J. / Wlodawer, A. / Gustchina, A.
Citation
Journal: Proteins / Year: 2000
Title: Structural studies of FIV and HIV-1 proteases complexed with an efficient inhibitor of FIV protease
Authors: Li, M. / Morris, G.M. / Lee, T. / Laco, G.S. / Wong, C.H. / Olson, A.J. / Elder, J.H. / Wlodawer, A. / Gustchina, A.
#1: Journal: Nat.Struct.Biol. / Year: 1995
Title: Structural Studies of HIV and Fiv Proteases Complexed with an Efficient Inhibitor of Fiv Pr
Authors: Wlodawer, A. / Gustchina, A. / Reshetnikova, L. / Lubkowski, J. / Zdanov, A. / Hui, K. / Angleton, E. / Farmerie, W. / Goodenow, M. / Bhatt, D. / Zhang, L. / Dunn, B.
History
DepositionDec 3, 1998Processing site: RCSB
Revision 1.0Dec 9, 1998Provider: repository / Type: Initial release
Revision 1.1Apr 26, 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 1.3Feb 27, 2013Group: Other
Revision 1.4Dec 27, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms / struct_conn / 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_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: PROTEIN (PROTEASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,7142
Polymers10,8051
Non-polymers9091
Water59433
1
A: PROTEIN (PROTEASE)
hetero molecules

A: PROTEIN (PROTEASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,4284
Polymers21,6102
Non-polymers1,8182
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation9_555-x,-x+y,-z+2/31
Buried area3450 Å2
ΔGint-22 kcal/mol
Surface area10020 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)63.202, 63.202, 83.464
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-301-

HOH

21A-323-

HOH

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Components

#1: Protein PROTEIN (PROTEASE)


Mass: 10804.808 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: COMPLEXED WITH TL-3-093
Source: (gene. exp.) Human immunodeficiency virus type 1 (CLONE 12)
Genus: Lentivirus / Species: Human immunodeficiency virus 1 / Production host: Escherichia coli (E. coli) / References: UniProt: P03366, HIV-1 retropepsin
#2: Chemical ChemComp-3TL / benzyl [(1S,4S,7S,8R,9R,10S,13S,16S)-7,10-dibenzyl-8,9-dihydroxy-1,16-dimethyl-4,13-bis(1-methylethyl)-2,5,12,15,18-pentaoxo-20-phenyl-19-oxa-3,6,11,14,17-pentaazaicos-1-yl]carbamate / TL-3, C2 symmetric inhibitor


Type: peptide-like, Peptide-like / Class: Inhibitor / Mass: 909.077 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C50H64N6O10
References: N-[(benzyloxy)carbonyl]-L-alanyl-N-[(1R)-1-benzyl-2-oxoethyl]-L-valinamide
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 33 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsTHE INHIBITOR IS A C2 SYMMETRIC HIV PROTEASE

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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: 2.2 Å3/Da / Density % sol: 44.4 %
Crystal growpH: 5.4
Details: SAMPLE: 3.0MG/ML HIVPR IN 25MM NAACETATE WITH 1MM EDTA AND 10MM DTT AT PH 5.5. WELL SOLUTION: 1.3M AMMONIUM SULFATE IN SODIUM ACETATE BUFFER AT PH 5.3 MIXING SAMPLE AND WELL SOLLUTION 1:1, pH 5.4
PH range: 5.3-5.5
Crystal grow
*PLUS
pH: 6.2 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
115 %satammonium sulfate1reservoir
285 mMsodium citrate1reservoiror 170 mM sodium phosphate
36 %MPD1reservoir
40.02 %sodium azide1reservoir

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Feb 1, 1998 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→20 Å / Num. obs: 8126 / % possible obs: 98.4 % / Observed criterion σ(I): 0 / Redundancy: 6.1 % / Rmerge(I) obs: 0.106 / Net I/σ(I): 10.5
Reflection shellResolution: 1.9→1.93 Å / Mean I/σ(I) obs: 2.6 / Rsym value: 0.419 / % possible all: 96.2
Reflection shell
*PLUS
% possible obs: 96.2 % / Rmerge(I) obs: 0.419

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Processing

Software
NameClassification
X-PLORmodel building
SHELXLrefinement
SHELXL-97refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementMethod to determine structure: OTHER / Resolution: 2→10 Å / Num. parameters: 3323 / Num. restraintsaints: 3233 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
Details: ANISOTROPIC SCALING APPLIED BY METHOD PF PARKIN, MOEZZI & HOPE, J.APPL.CRYST.28(1995)53-56
RfactorNum. reflection% reflectionSelection details
Rfree0.2809 755 11 %RANDOM
all0.195 6887 --
obs0.1881 -97.9 %-
Solvent computationSolvent model: MOEWS & KRETSINGER
Refine analyzeNum. disordered residues: 1 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 819.5
Refinement stepCycle: LAST / Resolution: 2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms752 0 33 33 818
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.006
X-RAY DIFFRACTIONs_angle_d0.024
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.025
X-RAY DIFFRACTIONs_zero_chiral_vol0.026
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.039
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.023
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.095
X-RAY DIFFRACTIONs_approx_iso_adps0
Software
*PLUS
Name: SHELXL-97 / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.195 / Rfactor Rfree: 0.281 / Rfactor Rwork: 0.186
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 34.53 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_angle_d0.023
X-RAY DIFFRACTIONs_plane_restr0.025
X-RAY DIFFRACTIONs_chiral_restr0.039

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