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- PDB-4fiv: FIV PROTEASE COMPLEXED WITH AN INHIBITOR LP-130 -

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Basic information

Entry
Database: PDB / ID: 4fiv
TitleFIV PROTEASE COMPLEXED WITH AN INHIBITOR LP-130
ComponentsFELINE IMMUNODEFICIENCY VIRUS PROTEASE
KeywordsASPARTIC PROTEASE / FIV / RETROPEPSIN / RETROVIRUS / CAT
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 / RNA-directed DNA polymerase ...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 / RNA-directed DNA polymerase / viral genome integration into host DNA / establishment of integrated proviral latency / RNA-directed DNA polymerase activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / RNA-DNA hybrid ribonuclease activity / DNA recombination / Hydrolases; Acting on ester bonds / aspartic-type endopeptidase activity / 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 / 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 / Cathepsin D, subunit A; domain 1 / Acid Proteases / 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-LP1 / Pol polyprotein / Pol polyprotein
Similarity search - Component
Biological speciesFeline immunodeficiency virus
MethodX-RAY DIFFRACTION / RIGID BODY REFINEMENT / Resolution: 1.8 Å
AuthorsKervinen, J. / Lubkowski, J. / Zdanov, A. / Wlodawer, A. / Gustchina, A.
CitationJournal: Protein Sci. / Year: 1998
Title: Toward a universal inhibitor of retroviral proteases: comparative analysis of the interactions of LP-130 complexed with proteases from HIV-1, FIV, and EIAV.
Authors: Kervinen, J. / Lubkowski, J. / Zdanov, A. / Bhatt, D. / Dunn, B.M. / Hui, K.Y. / Powell, D.J. / Kay, J. / Wlodawer, A. / Gustchina, A.
History
DepositionJul 15, 1998Processing site: BNL
Revision 1.0Jan 13, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 9, 2023Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Refinement description
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_special_symmetry / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Remark 650 HELIX DETERMINATION METHOD: TAKEN FROM RELEASED PDB ENTRY 1FIV
Remark 700 SHEET DETERMINATION METHOD: TAKEN FROM RELEASED PDB ENTRY 1FIV

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: FELINE IMMUNODEFICIENCY VIRUS PROTEASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,6382
Polymers12,8431
Non-polymers7951
Water1,65792
1
A: FELINE IMMUNODEFICIENCY VIRUS PROTEASE
hetero molecules

A: FELINE IMMUNODEFICIENCY VIRUS PROTEASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,2764
Polymers25,6862
Non-polymers1,5902
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+2/31
Buried area6710 Å2
ΔGint-53 kcal/mol
Surface area9470 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)50.650, 50.650, 74.500
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-201-

LP1

21A-301-

HOH

DetailsTHE AUTHORS NOTE THAT THIS MOLECULE IS ACTIVE AS DIMER

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Components

#1: Protein FELINE IMMUNODEFICIENCY VIRUS PROTEASE / FIV PR / RETROPEPSIN


Mass: 12842.825 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Feline immunodeficiency virus / Genus: Lentivirus / Production host: Escherichia coli (E. coli) / Strain (production host): PETALUMA
References: UniProt: P16088, UniProt: Q66972*PLUS, HIV-1 retropepsin
#2: Chemical ChemComp-LP1 / 4-[2-(2-ACETYLAMINO-3-NAPHTALEN-1-YL-PROPIONYLAMINO)-4-METHYL-PENTANOYLAMINO]-3-HYDROXY-6-METHYL-HEPTANOIC ACID [1-(1-CARBAMOYL-2-NAPHTHALEN-1-YL-ETHYLCARBAMOYL)-PROPYL]-AMIDE


Mass: 794.978 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C45H58N6O7
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 92 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsTHE INHIBITOR LP-130 (1NI 201) IS TWO-FOLD DISORDERED, SO THE TWO ORIENTATIONS FALL ON TOP OF EACH ...THE INHIBITOR LP-130 (1NI 201) IS TWO-FOLD DISORDERED, SO THE TWO ORIENTATIONS FALL ON TOP OF EACH OTHER. SOME ATOMS RELATED BY CRYSTALLOGRAPHIC SYMMETRY MAY BE IN CLOSE CONTACT. THE ALTERNATE LOCATION INDICATOR A HAS BEEN ASSIGNED TO THE DISORDERED INHIBITOR SO THAT THESE ATOMS WOULD NOT BE LISTED AS CLOSE CONTACTS.

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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: 2.15 Å3/Da / Density % sol: 43 %
Crystal growpH: 7.2 / Details: pH 7.2
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
15 mg/mlprotein1drop
320-25 %MPD1reservoir
450 mMimidazole/HCl1reservoir
51 mMEDTA1reservoir
61 mMdithiothreitol1reservoir
2DMSO1drop

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Sep 2, 1994 / Details: MIRRORS
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→40 Å / Num. obs: 9993 / % possible obs: 92.3 % / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Rmerge(I) obs: 0.092
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.273 / % possible all: 85.4
Reflection shell
*PLUS
% possible obs: 85.4 %

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Processing

Software
NameClassification
X-PLORmodel building
PROFFTrefinement
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementMethod to determine structure: RIGID BODY REFINEMENT
Starting model: PDB ENTRY 1FIV

1fiv


Resolution: 1.8→10 Å / σ(F): 3 /
RfactorNum. reflection
Rwork0.149 -
obs-9085
Refinement stepCycle: LAST / Resolution: 1.8→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms891 0 58 92 1041
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0140.017
X-RAY DIFFRACTIONp_angle_d0.0460.041
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0480.057
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.9672.4
X-RAY DIFFRACTIONp_mcangle_it2.6333.3
X-RAY DIFFRACTIONp_scbond_it3.9323.7
X-RAY DIFFRACTIONp_scangle_it5.3166.4
X-RAY DIFFRACTIONp_plane_restr0.0170.022
X-RAY DIFFRACTIONp_chiral_restr0.1750.18
X-RAY DIFFRACTIONp_singtor_nbd0.2210.5
X-RAY DIFFRACTIONp_multtor_nbd0.2340.5
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.2530.5
X-RAY DIFFRACTIONp_planar_tor3.43.4
X-RAY DIFFRACTIONp_staggered_tor16.413
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor39.720
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: PROFFT / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.149
Solvent computation
*PLUS
Displacement parameters
*PLUS

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