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- PDB-1fmb: EIAV PROTEASE COMPLEXED WITH THE INHIBITOR HBY-793 -

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Basic information

Entry
Database: PDB / ID: 1fmb
TitleEIAV PROTEASE COMPLEXED WITH THE INHIBITOR HBY-793
ComponentsEIAV PROTEASE
KeywordsHYDROLASE (ACID PROTEINASE) / RNA-DIRECTED DNA POLYMERASE / ASPARTYL PROTEASE / ENDONUCLEASE / POLYPROTEIN
Function / homology
Function and homology information


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 ...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 / proteolysis / DNA binding / zinc ion binding
Similarity search - Function
dUTPase-like / dUTPase / dUTPase, trimeric / dUTPase-like superfamily / Reverse transcriptase connection / Reverse transcriptase connection domain / Reverse transcriptase thumb / Reverse transcriptase thumb domain / Integrase Zinc binding domain / Zinc finger integrase-type profile. ...dUTPase-like / dUTPase / dUTPase, trimeric / dUTPase-like superfamily / 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. / RNase H / Integrase core domain / Integrase, catalytic core / Integrase catalytic domain profile. / 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-HYB / Pol polyprotein
Similarity search - Component
Biological speciesEquine infectious anemia virus
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsWlodawer, A. / Gustchina, A. / Zdanov, A. / Kervinen, J.
CitationJournal: Protein Sci. / Year: 1996
Title: Structure of equine infectious anemia virus proteinase complexed with an inhibitor.
Authors: Gustchina, A. / Kervinen, J. / Powell, D.J. / Zdanov, A. / Kay, J. / Wlodawer, A.
History
DepositionFeb 27, 1996Processing site: BNL
Revision 1.0Oct 14, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_struct_special_symmetry / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Feb 7, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.5Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: EIAV PROTEASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,9592
Polymers11,3921
Non-polymers5671
Water2,306128
1
A: EIAV PROTEASE
hetero molecules

A: EIAV PROTEASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,9184
Polymers22,7852
Non-polymers1,1342
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area5820 Å2
ΔGint-36 kcal/mol
Surface area9580 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)42.930, 45.710, 56.770
Angle α, β, γ (deg.)90.00, 110.50, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-201-

HYB

21A-301-

HOH

DetailsTHIS FILE CONTAINS ONLY A MONOMER, WHILE THE ACTIVE ENZYME IS A DIMER. IN ORDER TO CREATE A DIMERIC MOLECULE, CRYSTALLOGRAPHIC COORDINATES NEED TO BE TRANSFORMED TO (-X), Y, (-Z).

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Components

#1: Protein EIAV PROTEASE


Mass: 11392.265 Da / Num. of mol.: 1 / Mutation: I54G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Equine infectious anemia virus / Genus: Lentivirus / Plasmid: PET-226 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P32542, HIV-1 retropepsin
#2: Chemical ChemComp-HYB / [2-(2-METHYL-PROPANE-2-SULFONYLMETHYL)-3-NAPHTHALEN-1-YL-PROPIONYL-VALINYL]-PHENYLALANINOL


Mass: 566.751 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C32H42N2O5S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 128 / Source method: isolated from a natural source / Formula: H2O

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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: 2.29 Å3/Da / Density % sol: 46.27 %
Crystal growpH: 4.6 / Details: pH 4.6
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
13.6 mg/mlEIAV PR1drop
26 Murea1drop
320 mMpotassium phosphate1drop
420 %PEG40001reservoir
525 mMsodium acetate1reservoir
60.4 Mammonium sulfate1reservoir
70.1 %sodium azide1reservoir

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Data collection

DiffractionMean temperature: 273 K
Diffraction sourceWavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 4, 1995
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→20 Å / Num. obs: 8443 / % possible obs: 88.5 % / Observed criterion σ(I): 1 / Redundancy: 6.1 % / Rmerge(I) obs: 0.067
Reflection
*PLUS
Num. measured all: 59519

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: HIV-1 PROTEASE

Resolution: 1.8→20 Å / σ(F): 3
Details: THE TWO ORIENTATIONS OF THE INHIBITOR CREATED IN THE ACTIVE ENZYME OVERLAP WITH COMPLETE SUPERPOSITION AT THE PERIPHERY AND SOME DEVIATION IN THE CENTER. RESIDUES 56 - 57 HAVE BEEN MODELED ...Details: THE TWO ORIENTATIONS OF THE INHIBITOR CREATED IN THE ACTIVE ENZYME OVERLAP WITH COMPLETE SUPERPOSITION AT THE PERIPHERY AND SOME DEVIATION IN THE CENTER. RESIDUES 56 - 57 HAVE BEEN MODELED WITH TWO ORIENTATIONS OF THEIR MAIN CHAINS, SINCE THEY FORM ALTERNATE HYDROGEN BONDS, DUE TO THE SAME DISORDER PHENOMENON.
RfactorNum. reflection% reflection
Rwork0.136 --
obs-8140 85 %
Displacement parametersBiso mean: 19.12 Å2
Refinement stepCycle: LAST / Resolution: 1.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms791 0 40 128 959
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0140.017
X-RAY DIFFRACTIONp_angle_d0.0460.044
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0430.059
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.9162.5
X-RAY DIFFRACTIONp_mcangle_it2.5673.5
X-RAY DIFFRACTIONp_scbond_it3.724
X-RAY DIFFRACTIONp_scangle_it5.3287
X-RAY DIFFRACTIONp_plane_restr0.0180.022
X-RAY DIFFRACTIONp_chiral_restr0.1770.18
X-RAY DIFFRACTIONp_singtor_nbd0.2070.5
X-RAY DIFFRACTIONp_multtor_nbd0.450.5
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.3820.5
X-RAY DIFFRACTIONp_planar_tor3.43.5
X-RAY DIFFRACTIONp_staggered_tor19.114
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor32.412
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: PROFFT / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.136
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 22.2 Å2

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