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- PDB-1fiv: STRUCTURE OF AN INHIBITOR COMPLEX OF PROTEINASE FROM FELINE IMMUN... -

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Basic information

Entry
Database: PDB / ID: 1fiv
TitleSTRUCTURE OF AN INHIBITOR COMPLEX OF PROTEINASE FROM FELINE IMMUNODEFICIENCY VIRUS
Components
  • FIV PROTEASE
  • FIV PROTEASE INHIBITOR ACE-ALN-VAL-STA-GLU-ALN-NH2
KeywordsHYDROLASE/HYDROLASE INHIBITOR / ACID PROTEINASE / 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
FIV PROTEASE INHIBITOR LP-149; Ac-NA-Val-Sta-Glu-NA-NH2 / Pol polyprotein
Similarity search - Component
Biological speciesFeline immunodeficiency virus
MethodX-RAY DIFFRACTION / Resolution: 2 Å
AuthorsWlodawer, A. / Gustchina, A. / Reshetnikova, L. / Lubkowski, J. / Zdanov, A.
CitationJournal: 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.
History
DepositionMay 4, 1995Processing site: BNL
Revision 1.0Jul 31, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 3, 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 1, 2012Group: Derived calculations
Revision 1.4Dec 12, 2012Group: Other
Revision 1.5Jul 17, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Refinement description
Category: pdbx_database_status / pdbx_struct_special_symmetry ...pdbx_database_status / pdbx_struct_special_symmetry / software / struct_conn
Item: _pdbx_database_status.process_site / _software.classification / _struct_conn.pdbx_leaving_atom_flag
Revision 1.6Aug 14, 2019Group: Data collection / Refinement description / Category: software / Item: _software.classification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: FIV PROTEASE
B: FIV PROTEASE INHIBITOR ACE-ALN-VAL-STA-GLU-ALN-NH2


Theoretical massNumber of molelcules
Total (without water)13,6652
Polymers13,6652
Non-polymers00
Water1,69394
1
A: FIV PROTEASE
B: FIV PROTEASE INHIBITOR ACE-ALN-VAL-STA-GLU-ALN-NH2

A: FIV PROTEASE
B: FIV PROTEASE INHIBITOR ACE-ALN-VAL-STA-GLU-ALN-NH2


Theoretical massNumber of molelcules
Total (without water)27,3304
Polymers27,3304
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+2/31
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
11B-204-

STA

DetailsTHIS FILE CONTAINS ONLY A MONOMER. IN ORDER TO CREATE A DIMERIC MOLECULE, CRYSTALLOGRAPHIC COORDINATES NEED TO BE TRANSFORMED TO (X-Y), -Y, (2/3-Z).

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Components

#1: Protein FIV PROTEASE


Mass: 12842.825 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Feline immunodeficiency virus / Production host: Escherichia coli (E. coli) / References: UniProt: P16088, HIV-1 retropepsin
#2: Protein/peptide FIV PROTEASE INHIBITOR ACE-ALN-VAL-STA-GLU-ALN-NH2 / FIV PROTEASE INHIBITOR LP-149


Type: Peptide-like / Class: Inhibitor / Mass: 821.981 Da / Num. of mol.: 1 / Source method: obtained synthetically
References: FIV PROTEASE INHIBITOR LP-149; Ac-NA-Val-Sta-Glu-NA-NH2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 94 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHE INHIBITOR ACE-ALN-VAL-STA-GLU-ALN-NH2 IS DISORDERED AROUND THE TWO-FOLD CRYSTALLOGRAPHIC AXIS. ...THE INHIBITOR ACE-ALN-VAL-STA-GLU-ALN-NH2 IS DISORDERED AROUND THE TWO-FOLD CRYSTALLOGRAPHIC AXIS. APPLICATION OF CRYSTALLOGRAPHIC SYMMETRY RESULTS IN THE OVERLAP OF THE TWO ORIENTATIONS. THE OCCUPANCY OF EACH ORIENTATION IS 1/2.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.06 Å3/Da / Density % sol: 40.19 %
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 7.2 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
13-5 mg/mlprotein1drop
250 mMimidazole-HCl1drop
31 mMEDTA1drop
41 mMdithiothreitol1drop
55-10 %MPD1drop
620-25 %MPD1reservoir
750 mMimidazole-HCl1reservoir

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Data collection

DetectorDate: Sep 2, 1994
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionNum. obs: 7033 / % possible obs: 90 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.06
Reflection
*PLUS
Highest resolution: 2 Å / Num. measured all: 17555 / Rmerge(I) obs: 0.06

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Processing

Software
NameClassification
X-PLORmodel building
PROLSQrefinement
X-PLORrefinement
XENGENdata reduction
X-PLORphasing
RefinementResolution: 2→10 Å /
RfactorNum. reflection
Rwork0.148 -
obs0.148 6527
Refinement stepCycle: LAST / Resolution: 2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms961 0 0 94 1055
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.017
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_deg
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.2681.5
X-RAY DIFFRACTIONx_mcangle_it2.0042
X-RAY DIFFRACTIONx_scbond_it3.9083
X-RAY DIFFRACTIONx_scangle_it5.7674
Software
*PLUS
Name: PROLSQ / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal targetDev ideal
X-RAY DIFFRACTIONp_bond_d0.02
X-RAY DIFFRACTIONp_angle_d0.0350.047
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_dihedral_angle_d
X-RAY DIFFRACTIONp_improper_angle_d
X-RAY DIFFRACTIONp_planar_d0.050.047
X-RAY DIFFRACTIONp_chiral_restr0.150.151
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scangle_it

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