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- PDB-6fiv: STRUCTURAL STUDIES OF HIV AND FIV PROTEASES COMPLEXED WITH AN EFF... -

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Basic information

Entry
Database: PDB / ID: 6fiv
TitleSTRUCTURAL STUDIES OF HIV AND FIV PROTEASES COMPLEXED WITH AN EFFICIENT INHIBITOR OF FIV PR
ComponentsRETROPEPSIN
KeywordsHYDROLASE/HYDROLASE INHIBITOR / FIV PROTEASE / HYDROLASE-HYDROLASE INHIBITOR COMPLEX
Function / homology
Function and homology information


dUTP catabolic process / dUMP biosynthetic process / dUTP diphosphatase / dUTP diphosphatase activity / Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / DNA integration / viral genome integration into host DNA ...dUTP catabolic process / dUMP biosynthetic process / dUTP diphosphatase / dUTP diphosphatase activity / Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / RNA stem-loop binding / RNA-directed DNA polymerase activity / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / DNA recombination / aspartic-type endopeptidase activity / Hydrolases; Acting on ester bonds / symbiont entry into host cell / magnesium ion binding / proteolysis / DNA binding / zinc ion binding
Similarity search - Function
Deoxyuridine triphosphate nucleotidohydrolase / dUTPase-like / dUTPase / dUTPase, trimeric / dUTPase-like superfamily / Reverse transcriptase connection / Reverse transcriptase connection domain / Reverse transcriptase thumb / Reverse transcriptase thumb domain / Zinc finger integrase-type profile. ...Deoxyuridine triphosphate nucleotidohydrolase / dUTPase-like / dUTPase / dUTPase, trimeric / dUTPase-like superfamily / Reverse transcriptase connection / Reverse transcriptase connection domain / Reverse transcriptase thumb / Reverse transcriptase thumb 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. / RNase H / Integrase core domain / Integrase, catalytic core / Integrase catalytic domain profile. / Retropepsin-like catalytic 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. / Cathepsin D, subunit A; domain 1 / Acid Proteases / 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 / Pol polyprotein
Similarity search - Component
Biological speciesFeline immunodeficiency virus
MethodX-RAY DIFFRACTION / OTHER / Resolution: 1.9 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 2, 1998Deposition site: BNL / Processing 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 / Source and taxonomy / 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_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RETROPEPSIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,8193
Polymers12,8141
Non-polymers1,0052
Water1,36976
1
A: RETROPEPSIN
hetero molecules

A: RETROPEPSIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,6386
Polymers25,6282
Non-polymers2,0104
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+2/31
Buried area3960 Å2
ΔGint-50 kcal/mol
Surface area10580 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)50.760, 50.760, 73.360
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-301-

HOH

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Components

#1: Protein RETROPEPSIN


Mass: 12813.828 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: COMPLEXED WITH TL-3-093 / Source: (gene. exp.) Feline immunodeficiency virus / Genus: Lentivirus / Strain: (isolate Petaluma) / Production host: Escherichia coli (E. coli) / References: UniProt: P16088, HIV-1 retropepsin
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: 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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 76 / 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
Details: SAMPLE: 3.4MG/ML Q99V IN 25MM IMIDAZOL BUFFER AT PH 7.0 WITH 1MM EDTA AND 10MM DTT. WELL SOLUTION: 1.6M AMMONIUM SULFATE IN SODIUM ACETATE BUFFER AT PH 4.5 MIXING SAMPLE AND WELL SOLLUTION 1:1, pH 5.0
PH range: 4.5-7.0
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 7 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
17 mg/mlTL-31drop
250 mMimidazole-HCl1drop
31 mMEDTA1drop
41 mMdithiothreitol1drop
52 Mammonium sulfate1drop
60.1 Msodium acetate1drop
72 Mammonium sulfate1reservoir
80.1 Msodium acetate1reservoir

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: SIEMENS HI-STAR / Detector: AREA DETECTOR / Date: Nov 1, 1997
RadiationMonochromator: GRAPHITE / Protocol: 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: 8437 / % possible obs: 3.1 % / Observed criterion σ(I): 0 / Redundancy: 6.3 % / Rmerge(I) obs: 0.078
Reflection shellResolution: 1.9→1.97 Å / Rmerge(I) obs: 0.372 / Mean I/σ(I) obs: 1.98 / % possible all: 75
Reflection
*PLUS
% possible obs: 93.1 %
Reflection shell
*PLUS
% possible obs: 75 %

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Processing

Software
NameClassification
X-PLORmodel building
SHELXLrefinement
SHELXL-97refinement
SAINTdata reduction
SAINTdata scaling
X-PLORphasing
RefinementMethod to determine structure: OTHER / Resolution: 1.9→10 Å / Num. parameters: 4069 / Num. restraintsaints: 3813 / 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
Rfree0.2657 879 11.9 %RANDOM
all0.1551 7385 --
obs0.1573 -82.5 %-
Solvent computationSolvent model: MOEWS & KRETSINGER
Refine analyzeNum. disordered residues: 2 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 991
Refinement stepCycle: LAST / Resolution: 1.9→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms891 0 38 76 1005
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_planes0.027
X-RAY DIFFRACTIONs_zero_chiral_vol0.03
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.041
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.007
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.089
X-RAY DIFFRACTIONs_approx_iso_adps0
Software
*PLUS
Name: SHELXL-97 / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.155 / Rfactor Rfree: 0.266 / Rfactor Rwork: 0.157
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 25.39 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_plane_restr0.027
X-RAY DIFFRACTIONs_chiral_restr0.041

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