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- PDB-3fiv: CRYSTAL STRUCTURE OF FELINE IMMUNODEFICIENCY VIRUS PROTEASE COMPL... -

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Basic information

Entry
Database: PDB / ID: 3fiv
TitleCRYSTAL STRUCTURE OF FELINE IMMUNODEFICIENCY VIRUS PROTEASE COMPLEXED WITH A SUBSTRATE
Components
  • ACE-ALN-VAL-LEU-ALA-GLU-ALN-NH2
  • FELINE IMMUNODEFICIENCY VIRUS PROTEASE
KeywordsHYDROLASE/HYDROLASE INHIBITOR / ASPARTIC PROTEASE / RETROVIRAL 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-directed DNA polymerase activity / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / 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
N-acetyl-3-(naphthalen-1-yl)-L-alanyl-L-valyl-L-leucyl-L-alanyl-L-alpha-glutamyl-3-naphthalen-1-yl- L-alaninamide / Pol polyprotein
Similarity search - Component
Biological speciesFeline immunodeficiency virus
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsSchalk-Hihi, C. / Lubkowski, J. / Zdanov, A. / Wlodawer, A. / Gustchina, A.
Citation
Journal: Biochemistry / Year: 1997
Title: Crystal structures of the inactive D30N mutant of feline immunodeficiency virus protease complexed with a substrate and an inhibitor.
Authors: Laco, G.S. / Schalk-Hihi, C. / Lubkowski, J. / Morris, G. / Zdanov, A. / Olson, A. / Elder, J.H. / Wlodawer, A. / Gustchina, A.
#1: Journal: Nat.Struct.Biol. / Year: 1995
Title: Structure of an Inhibitor Complex of the Proteinase from Feline Immunodeficiency Virus
Authors: Wlodawer, A. / Gustchina, A. / Reshetnikova, L. / Lubkowski, J. / Zdanov, A. / Hui, K.Y. / Angleton, E.L. / Farmerie, W.G. / Goodenow, M.M. / Bhatt, D. / Zhang, L. / Dunn, B.M.
History
DepositionJul 9, 1997Processing site: BNL
Revision 1.0Nov 12, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 21, 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 1.3Dec 12, 2012Group: Other
Revision 1.4Aug 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 / 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 / _pdbx_database_status.process_site / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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: FELINE IMMUNODEFICIENCY VIRUS PROTEASE
B: FELINE IMMUNODEFICIENCY VIRUS PROTEASE
I: ACE-ALN-VAL-LEU-ALA-GLU-ALN-NH2
J: ACE-ALN-VAL-LEU-ALA-GLU-ALN-NH2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,4516
Polymers28,2594
Non-polymers1922
Water2,666148
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.890, 50.890, 74.530
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

#1: Protein FELINE IMMUNODEFICIENCY VIRUS PROTEASE / FIV PR


Mass: 13280.297 Da / Num. of mol.: 2 / Mutation: D30N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Feline immunodeficiency virus / Genus: Lentivirus / Cell line: BL21 / Plasmid: BL21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) PLYSS / References: UniProt: P16088, HIV-1 retropepsin
#2: Protein/peptide ACE-ALN-VAL-LEU-ALA-GLU-ALN-NH2 / FIV PROTEASE INHIBITOR LP-149


Type: Peptide-like / Class: Inhibitor / Mass: 849.007 Da / Num. of mol.: 2 / Source method: obtained synthetically
References: N-acetyl-3-(naphthalen-1-yl)-L-alanyl-L-valyl-L-leucyl-L-alanyl-L-alpha-glutamyl-3-naphthalen-1-yl- L-alaninamide
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 148 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHE INHIBITOR ACE-ALN-VAL-LEU-ALA-GLU-ALN-NH2 IS DISORDERED. IT APPEARS IN TWO ORIENTATIONS (CHAINS ...THE INHIBITOR ACE-ALN-VAL-LEU-ALA-GLU-ALN-NH2 IS DISORDERED. IT APPEARS IN TWO ORIENTATIONS (CHAINS I AND J) THAT ARE RELATED BY NON-CRYSTALLOGRAPHIC SYMMETRY. THE OCCUPANCY OF EACH ORIENTATION IS 1/2.

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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: 2.05 Å3/Da / Density % sol: 37.61 %
Crystal growpH: 5.6
Details: PROTEIN WAS CRYSTALLIZED FROM 2.0 M AMMONIUM SULFATE, 0.1 M SODIUM ACETATE, PH=5.6. PROTEIN CONCENTRATION, 5.0 MG/ML. CRYSTALLIZATION METHOD: HANGING DROP VAPOR DIFFUSION
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 7 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
27 mg/mlLP-1491drop
35 mg/mlsubstrate1drop
450 mMimidazol-hydrochloride1drop
51 mMEDTA1drop
61 mMdithiothreitol1drop
72 Mammonium sulfate1reservoir
80.1 Msodium acetate1reservoir
1FIV PR1drop0.0025ml

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR591 / Wavelength: 1.5418
DetectorType: MACSCIENCE / Detector: IMAGE PLATE / Date: Apr 23, 1996 / Details: MIRRORS
RadiationMonochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→20 Å / Num. obs: 40465 / % possible obs: 87.2 % / Observed criterion σ(I): 1 / Redundancy: 2.32 % / Rsym value: 0.091 / Net I/σ(I): 16
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 1.65 % / Mean I/σ(I) obs: 2.59 / Rsym value: 0.42 / % possible all: 60.8
Reflection
*PLUS
Num. obs: 17411 / Num. measured all: 40465 / Rmerge(I) obs: 0.091
Reflection shell
*PLUS
% possible obs: 68.5 %

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1FIV

1fiv


Resolution: 1.85→8 Å / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / σ(F): 3
Details: HUBER AND ENGH PARAMETERS WERE USED IN THE REFINEMENT. FOR NON-STANDARD RESIDUES (CYO, ALN, NAM, ACE, SO4) LIBRARIES BASED ON EXISTING PARAMETERS WERE CREATED BY SIMILARITY. THE X-RAY DATA ...Details: HUBER AND ENGH PARAMETERS WERE USED IN THE REFINEMENT. FOR NON-STANDARD RESIDUES (CYO, ALN, NAM, ACE, SO4) LIBRARIES BASED ON EXISTING PARAMETERS WERE CREATED BY SIMILARITY. THE X-RAY DATA ARE COMPATIBLE WITH THE SPACE GROUP P31 2 1. THE LOWER SYMMETRY SPACE GROUP WAS UTILIZED IN REFINEMENT FOR TECHNICAL REASONS. THE CHAINS A AND B (AND I AND J) ARE THUS RELATED BY NON-CRYSTALLOGRAPHIC SYMMETRY, EQUIVALENT TO TWO-FOLD AXIS DIFFERENTIATING THE TWO SPACE GROUPS. THE Z VALUE IS GIVEN ON THE ASSUMPTION OF IDENTITY OF CHAINS A AND B.
RfactorNum. reflection% reflection
Rwork0.172 --
obs0.172 15187 89.5 %
Displacement parametersBiso mean: 28 Å2
Refinement stepCycle: LAST / Resolution: 1.85→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1900 0 10 148 2058
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.014
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.82
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d27.6
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.52
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it3.1381.5
X-RAY DIFFRACTIONx_mcangle_it3.3042
X-RAY DIFFRACTIONx_scbond_it3.1382
X-RAY DIFFRACTIONx_scangle_it3.3042.5
Refine LS restraints NCSNCS model details: RESTRAINTS / Rms dev Biso : 1.35 Å2 / Rms dev position: 0.005 Å / Weight Biso : 0.5 / Weight position: 1000
LS refinement shellResolution: 1.85→1.93 Å / Total num. of bins used: 8 /
RfactorNum. reflection
Rwork0.311 1307
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2TOPH19.PEP
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg27.6
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.52

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