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- PDB-1wbk: HIV-1 protease in complex with asymmetric inhibitor, BEA568 -

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Basic information

Entry
Database: PDB / ID: 1wbk
TitleHIV-1 protease in complex with asymmetric inhibitor, BEA568
ComponentsPOL PROTEIN (FRAGMENT)
KeywordsHYDROLASE/INHIBITOR / HYDROLASE-INHIBITOR COMPLEX / AIDS / ASPARTYL PROTEASE / DIMER / HYDROLASE / HYDROLASE/HYDROLASE INHIBITOR / PROTEIN-INHIBITOR COMPLEX
Function / homology
Function and homology information


aspartic-type endopeptidase activity / proteolysis
Similarity search - Function
Retropepsin-like catalytic domain / 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. / Aspartic peptidase domain superfamily ...Retropepsin-like catalytic domain / 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. / Aspartic peptidase domain superfamily / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Chem-568 / Pol protein
Similarity search - Component
Biological speciesHUMAN IMMUNODEFICIENCY VIRUS 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsLindberg, J. / Unge, T.
Citation
Journal: To be Published
Title: HIV-1 Protease in Complex with Asymmetric Inhibitor, Bea568
Authors: Lindberg, J. / Unge, T.
#1: Journal: Bioorg.Med.Chem. / Year: 2003
Title: Design and Synthesis of HIV-1 Protease Inhibitors. Novel Tetrahydrofuran P2 and P2'-Groups Interacting with Asp29 and 30 of the HIV-1 Protease. Determination of Binding from X-Ray Crystal ...Title: Design and Synthesis of HIV-1 Protease Inhibitors. Novel Tetrahydrofuran P2 and P2'-Groups Interacting with Asp29 and 30 of the HIV-1 Protease. Determination of Binding from X-Ray Crystal Structure of Inhibitor Protease Complex
Authors: Oscarsson, K. / Lahmann, M. / Lindberg, J. / Kangasmetsae, J. / Unge, T. / Oscarson, S. / Hallberg, A. / Samuelsson, B.
History
DepositionNov 2, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 4, 2004Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 17, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 7-STRANDED BARREL THIS IS REPRESENTED BY A 8-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "BA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 7-STRANDED BARREL THIS IS REPRESENTED BY A 8-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: POL PROTEIN (FRAGMENT)
B: POL PROTEIN (FRAGMENT)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,2283
Polymers21,6082
Non-polymers6211
Water1,51384
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)58.966, 86.750, 46.858
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein POL PROTEIN (FRAGMENT) / HIV-1 PROTEASE


Mass: 10803.756 Da / Num. of mol.: 2 / Fragment: RESIDUES 1-99
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HUMAN IMMUNODEFICIENCY VIRUS 1 / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q8Q3H0
#2: Chemical ChemComp-568 / N,N-[2,5-O-DIBENZYL-GLUCARYL]-DI-[1-AMINO-INDAN-2-OL]


Mass: 620.689 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H40N2O9
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 84 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.77 Å3/Da / Density % sol: 55.65 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 1.076
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.076 Å / Relative weight: 1
ReflectionResolution: 2→25 Å / Num. obs: 189607 / % possible obs: 98.8 % / Observed criterion σ(I): 2 / Redundancy: 2 % / Rmerge(I) obs: 0.08
Reflection shellResolution: 2→2.03 Å / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 3 / % possible all: 96.7

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Processing

SoftwareName: CNS / Version: 1.1 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→50 Å / Data cutoff high absF: 10000 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2355 831 4.9 %RANDOM
Rwork0.1938 ---
obs0.1938 16476 97.7 %-
Solvent computationBsol: 38.8404 Å2 / ksol: 0.31411 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.041 Å20 Å20 Å2
2--2.79 Å20 Å2
3----1.749 Å2
Refinement stepCycle: LAST / Resolution: 2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1516 0 45 84 1645
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006272
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.17196
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA_REP.PARAMDNA-RNA.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP
X-RAY DIFFRACTION5568.PAR568.TOP

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