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- PDB-1bai: Crystal structure of Rous sarcoma virus protease in complex with ... -

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Basic information

Entry
Database: PDB / ID: 1bai
TitleCrystal structure of Rous sarcoma virus protease in complex with inhibitor
ComponentsPROTEASE
KeywordsHYDROLASE/HYDROLASE INHIBITOR / PROTEIN-MEDIATED INTERACTION / VIRAL MATURATION / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


reverse transcription / host cell nucleoplasm / viral procapsid maturation / host cell nucleolus / Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / ribonuclease H / DNA integration / RNA-directed DNA polymerase / viral genome integration into host DNA / establishment of integrated proviral latency ...reverse transcription / host cell nucleoplasm / viral procapsid maturation / host cell nucleolus / Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / ribonuclease H / DNA integration / RNA-directed DNA polymerase / viral genome integration into host DNA / establishment of integrated proviral latency / viral capsid / RNA-directed DNA polymerase activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / RNA-DNA hybrid ribonuclease activity / viral nucleocapsid / DNA recombination / structural constituent of virion / Hydrolases; Acting on ester bonds / nucleic acid binding / DNA-directed DNA polymerase / aspartic-type endopeptidase activity / DNA-directed DNA polymerase activity / symbiont entry into host cell / host cell plasma membrane / proteolysis / DNA binding / RNA binding / zinc ion binding / membrane
Similarity search - Function
Retroviral nucleocapsid Gag protein p24, N-terminal / Retroviral Gag polyprotein, M / Retroviral M domain / gag protein p24 N-terminal 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 ...Retroviral nucleocapsid Gag protein p24, N-terminal / Retroviral Gag polyprotein, M / Retroviral M domain / gag protein p24 N-terminal 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. / Integrase core domain / Integrase, catalytic core / Integrase catalytic domain profile. / Retropepsin-like catalytic domain / Matrix protein, lentiviral and alpha-retroviral, N-terminal / 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 / Retrovirus capsid, C-terminal / Retroviral matrix protein / Retrovirus capsid, N-terminal / zinc finger / Zinc knuckle / Zinc finger, CCHC-type superfamily / Cathepsin D, subunit A; domain 1 / Acid Proteases / Zinc finger, CCHC-type / Zinc finger CCHC-type profile. / Ribonuclease H superfamily / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / 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-[(2R)-2-({N~5~-[amino(iminio)methyl]-L-ornithyl-L-valyl}amino)-4-methylpentyl]-L-phenylalanyl-L-alpha-glutamyl- L-alanyl-L-norleucinamide / Chem-0Q4 / Gag-Pol polyprotein / Gag polyprotein
Similarity search - Component
Biological speciesRous sarcoma virus
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsWu, J. / Adomat, J.M. / Ridky, T.W. / Louis, J.M. / Leis, J. / Harrison, R.W. / Weber, I.T.
CitationJournal: Biochemistry / Year: 1998
Title: Structural basis for specificity of retroviral proteases.
Authors: Wu, J. / Adomat, J.M. / Ridky, T.W. / Louis, J.M. / Leis, J. / Harrison, R.W. / Weber, I.T.
History
DepositionApr 17, 1998Processing site: BNL
Revision 1.0Jan 13, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 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 1.4Feb 7, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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 1.5Mar 13, 2024Group: Source and taxonomy / Structure summary / Category: entity / pdbx_entity_src_syn / Item: _entity.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROTEASE
B: PROTEASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,1313
Polymers27,2982
Non-polymers8331
Water1,53185
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5570 Å2
ΔGint-25 kcal/mol
Surface area11730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.610, 62.610, 132.150
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein PROTEASE /


Mass: 13648.806 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Rous sarcoma virus / References: UniProt: O92805, UniProt: P03322*PLUS
#2: Chemical ChemComp-0Q4 / N-[(2R)-2-({N~5~-[amino(iminio)methyl]-L-ornithyl-L-valyl}amino)-4-methylpentyl]-L-phenylalanyl-L-alpha-glutamyl-L-alanyl-L-norleucinamide / Inhibitor analogues of CA-p2


Type: peptide-like, Peptide-like / Class: Inhibitor / Mass: 833.053 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C40H70N11O8 / Details: PURIFIED FROM THE INCLUSION BODY FRACTION
References: N-[(2R)-2-({N~5~-[amino(iminio)methyl]-L-ornithyl-L-valyl}amino)-4-methylpentyl]-L-phenylalanyl-L-alpha-glutamyl- L-alanyl-L-norleucinamide
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 85 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsPEPTIDE INHIBITOR 0Q4 HAS A REDUCED PEPTIDE (-CH2-NH) INSTEAD OF THE NORMAL PEPTIDE LINK (-CO-NH).

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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: 2.66 Å3/Da / Density % sol: 53.67 %
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
10.23 mMprotease1drop
20.3 mMinhibitor1drop
310 %satammonium sulfate1reservoir

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Aug 15, 1996 / Details: MIRRORS
RadiationMonochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→8 Å / Num. obs: 9601 / % possible obs: 76.8 % / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.0943 / Rsym value: 0.175
Reflection shellResolution: 2.4→2.51 Å

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
R-AXISdata reduction
R-AXISdata scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→8 Å / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.293 --RANDOM
Rwork0.175 ---
obs0.175 9273 76.8 %-
Displacement parametersBiso mean: 18.5 Å2
Refinement stepCycle: LAST / Resolution: 2.4→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1910 0 59 85 2054
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.018
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_deg2.56
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d26.59
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d2.12
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 2.4→2.51 Å / Total num. of bins used: 8 /
RfactorNum. reflection
Rfree0.2441 98
Rwork0.175 852
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARACSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM19.SOLTOPH19.SOL
X-RAY DIFFRACTION3
X-RAY DIFFRACTION4
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.175 / Rfactor Rfree: 0.293 / Rfactor Rwork: 0.175
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg26.59
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg2.12
LS refinement shell
*PLUS
Rfactor Rfree: 0.244 / Num. reflection Rfree: 98 / Rfactor Rwork: 0.175

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