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- PDB-1bdl: HIV-1 (2:31-37) PROTEASE COMPLEXED WITH INHIBITOR SB203386 -

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Basic information

Entry
Database: PDB / ID: 1bdl
TitleHIV-1 (2:31-37) PROTEASE COMPLEXED WITH INHIBITOR SB203386
ComponentsHIV-1 PROTEASE
KeywordsHYDROLASE / AIDS / POLYPROTEIN / ASPARTYL PROTEASE / ACID PROTEASE / HYDROXYETHYLENE ISOSTERE INHIBITOR / SUBSTRATE ANALOGUE INHIBITOR
Function / homology
Function and homology information


HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / host multivesicular body / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency ...HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / host multivesicular body / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / telomerase activity / viral penetration into host nucleus / RNA stem-loop binding / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / host cell / viral nucleocapsid / DNA recombination / DNA-directed DNA polymerase / aspartic-type endopeptidase activity / Hydrolases; Acting on ester bonds / DNA-directed DNA polymerase activity / symbiont-mediated suppression of host gene expression / symbiont entry into host cell / viral translational frameshifting / lipid binding / host cell nucleus / host cell plasma membrane / virion membrane / structural molecule activity / proteolysis / DNA binding / zinc ion binding / membrane
Similarity search - Function
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 ...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. / Immunodeficiency lentiviral matrix, N-terminal / gag gene protein p17 (matrix protein) / RNase H / Integrase core domain / Integrase, catalytic core / Integrase catalytic domain profile. / Retropepsin-like catalytic domain / Matrix protein, lentiviral and alpha-retroviral, N-terminal / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / RNase H type-1 domain profile. / Ribonuclease H domain / Retropepsins / Retroviral aspartyl protease / Aspartyl protease, retroviral-type family profile. / Peptidase A2A, retrovirus, catalytic / Reverse transcriptase domain / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase (RT) catalytic domain profile. / Retrovirus capsid, C-terminal / Retroviral matrix protein / Cathepsin D, subunit A; domain 1 / Acid Proteases / Retrovirus capsid, N-terminal / zinc finger / Zinc knuckle / Zinc finger, CCHC-type superfamily / Zinc finger, CCHC-type / Zinc finger CCHC-type profile. / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Aspartic peptidase domain superfamily / Ribonuclease H superfamily / Ribonuclease H-like superfamily / Reverse transcriptase/Diguanylate cyclase domain / DNA/RNA polymerase superfamily / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Chem-IM1 / Gag-Pol polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / DIFFERENCE FOURIER / Resolution: 2.8 Å
AuthorsSwairjo, M.A. / Abdel-Meguid, S.S.
Citation
Journal: Biochemistry / Year: 1998
Title: Structural role of the 30's loop in determining the ligand specificity of the human immunodeficiency virus protease.
Authors: Swairjo, M.A. / Towler, E.M. / Debouck, C. / Abdel-Meguid, S.S.
#1: Journal: Biochemistry / Year: 1997
Title: Identification of a Loop Outside the Active Site Cavity of the Human Immunodeficiency Virus Proteases which Confers Inhibitor Specificity
Authors: Towler, E.M. / Thompson, S.K. / Tomaszek, T. / Debouck, C.
History
DepositionMay 10, 1998Processing site: BNL
Revision 1.0Aug 12, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...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 1.4Aug 2, 2023Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 1.5May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HIV-1 PROTEASE
B: HIV-1 PROTEASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,4374
Polymers21,3672
Non-polymers1,0692
Water724
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5640 Å2
ΔGint-30 kcal/mol
Surface area9840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.410, 63.410, 83.550
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Protein HIV-1 PROTEASE


Mass: 10683.631 Da / Num. of mol.: 2 / Mutation: T31S, V32I, L33V, E34A, E35G, M36I, S37E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Genus: Lentivirus / Strain: IIIB / Gene: HIV-1 PROTEASE / Plasmid: POTSKF33 / Gene (production host): HIV-1 PROTEASE / Production host: Escherichia coli (E. coli) / Strain (production host): IIIB STRAIN / Variant (production host): BMH 71-18 MUTS / References: UniProt: P04587, HIV-1 retropepsin
#2: Chemical ChemComp-IM1 / (2R,4S,5S,1'S)-2-PHENYLMETHYL-4-HYDROXY-5-(TERT-BUTOXYCARBONYL)AMINO-6-PHENYL HEXANOYL-N-(1'-IMIDAZO-2-YL)-2'-METHYLPROPANAMIDE


Mass: 534.690 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C31H42N4O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / 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: 2.22 Å3/Da / Density % sol: 45 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 6
Details: HANGING DROP VAPOUR DIFFUSION, BY MIXING EQUAL VOLUMES OF RESERVOIR AND SAMPLE, 21 DEGREES C. RESERVOIR: 10% PEG-1000, 0.2M AMMONIUM SULFATE, 0.1 M MES, PH 6.0. SAMPLE: 3.5 MG/ML ...Details: HANGING DROP VAPOUR DIFFUSION, BY MIXING EQUAL VOLUMES OF RESERVOIR AND SAMPLE, 21 DEGREES C. RESERVOIR: 10% PEG-1000, 0.2M AMMONIUM SULFATE, 0.1 M MES, PH 6.0. SAMPLE: 3.5 MG/ML PROTEIN/INHIBITOR COMPLEX AT 1:5 MOLAR RATIO., vapor diffusion - hanging drop
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 21 ℃ / pH: 5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 %PEG10001reservoir
20.2 Mammonium sulfate1reservoir
30.1 MMES1reservoir
43.5 mg/mlinhibitor1drop
5200 mM1dropNaCl
65 mMdithiothreitol1drop
72 mMEDTA1drop
850 mM1dropNaAc

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Data collection

DiffractionMean temperature: 292 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 1, 1997 / Details: MIRRORS
RadiationMonochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.8→20 Å / Num. obs: 4054 / % possible obs: 95.6 % / Observed criterion σ(I): 1 / Redundancy: 2.9 % / Rmerge(I) obs: 0.13 / Rsym value: 0.13
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 2.87 % / Rmerge(I) obs: 0.08 / Rsym value: 0.08 / % possible all: 74.2
Reflection
*PLUS
Num. measured all: 53648
Reflection shell
*PLUS
% possible obs: 74.2 %

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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: DIFFERENCE FOURIER
Starting model: PDB ENTRY 1SBG

1sbg


Resolution: 2.8→20 Å / Rfactor Rfree error: 0.02 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.255 412 10 %RANDOM
Rwork0.201 ---
obs-4054 95.6 %-
Displacement parametersBiso mean: 17.5 Å2
Baniso -1Baniso -2Baniso -3
1-17.5 Å217.5 Å217.5 Å2
2--17.5 Å217.5 Å2
3---17.5 Å2
Refine analyzeLuzzati coordinate error obs: 0.25 Å
Refinement stepCycle: LAST / Resolution: 2.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1502 0 78 4 1584
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.019
X-RAY DIFFRACTIONo_bond_d_na
X-RAY DIFFRACTIONo_bond_d_prot
X-RAY DIFFRACTIONo_angle_d
X-RAY DIFFRACTIONo_angle_d_na
X-RAY DIFFRACTIONo_angle_d_prot
X-RAY DIFFRACTIONo_angle_deg3.4
X-RAY DIFFRACTIONo_angle_deg_na
X-RAY DIFFRACTIONo_angle_deg_prot
X-RAY DIFFRACTIONo_dihedral_angle_d29.2
X-RAY DIFFRACTIONo_dihedral_angle_d_na
X-RAY DIFFRACTIONo_dihedral_angle_d_prot
X-RAY DIFFRACTIONo_improper_angle_d1.8
X-RAY DIFFRACTIONo_improper_angle_d_na
X-RAY DIFFRACTIONo_improper_angle_d_prot
X-RAY DIFFRACTIONo_mcbond_it
X-RAY DIFFRACTIONo_mcangle_it
X-RAY DIFFRACTIONo_scbond_it
X-RAY DIFFRACTIONo_scangle_it
LS refinement shellResolution: 2.8→2.93 Å / Total num. of bins used: 8 /
Num. reflection% reflection
Rwork400 -
obs-74 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM19.SOLTOPH19.SOL
X-RAY DIFFRACTION3IM1.PARAMIM1.TOPOL
X-RAY DIFFRACTION4PARAM19X.PROTOPH19X.PRO
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.201
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 19.6 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_deg
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg29.2
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.8
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scangle_it

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