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- PDB-2hc0: Structure of HIV protease 6X mutant in complex with AB-2. -

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Basic information

Entry
Database: PDB / ID: 2hc0
TitleStructure of HIV protease 6X mutant in complex with AB-2.
ComponentsProtease
KeywordsHYDROLASE / HIV / protease / mutant / aspartyl
Function / homology
Function and homology information


HIV-1 retropepsin / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / host multivesicular body / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / viral penetration into host nucleus / establishment of integrated proviral latency ...HIV-1 retropepsin / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / host multivesicular body / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / viral penetration into host nucleus / establishment of integrated proviral latency / RNA stem-loop binding / RNA-directed DNA polymerase activity / host cell / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / symbiont-mediated suppression of host gene expression / viral nucleocapsid / DNA recombination / DNA-directed DNA polymerase / Hydrolases; Acting on ester bonds / aspartic-type endopeptidase activity / DNA-directed DNA polymerase activity / symbiont entry into host cell / 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. / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / 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. / 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-AB2 / BROMIDE ION / Gag-Pol polyprotein / Protease
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsHeaslet, H. / Brik, A. / Lin, Y.-C. / Elder, J.H. / Stout, C.D.
CitationJournal: To be Published
Title: Structure of HIV Protease 6X Mutant in complex with AB-2
Authors: Heaslet, H. / Brik, A. / Lin, Y.-C. / Elder, J.H. / Stout, C.D.
History
DepositionJun 14, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 26, 2007Provider: repository / Type: Initial release
Revision 1.1Apr 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / 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 / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999SEQUENCE Mutations at positions 1024,1046,1053,1063,1077,1082 chain A and ...SEQUENCE Mutations at positions 1024,1046,1053,1063,1077,1082 chain A and 2124,2146,2153,2163,2177,2182 chain B are results of drug resistance selection. The Gln1007/2107Lys mutations were added to prevent autoproteolysis.

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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)23,12215
Polymers21,4992
Non-polymers1,62313
Water5,278293
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6450 Å2
ΔGint-21 kcal/mol
Surface area9360 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)86.610, 86.610, 33.660
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number78
Space group name H-MP43

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Components

#1: Protein Protease


Mass: 10749.708 Da / Num. of mol.: 2 / Fragment: residues 500-598 / Mutation: L24I, M46I, F53L, L63P, V77I, V82A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Genus: Lentivirus / Strain: NL4-3 / Gene: gag-pol / Plasmid: PET 21A+ / Production host: Escherichia coli (E. coli) / Strain (production host): BL21.DE3, PLYS S
References: UniProt: P03367, UniProt: Q9E3M8*PLUS, HIV-1 retropepsin
#2: Chemical
ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Br
#3: Chemical ChemComp-AB2 / [1-((1S,2R)-1-BENZYL-2-HYDROXY-3-{ISOBUTYL[(4-METHOXYPHENYL)SULFONYL]AMINO}PROPYL)-1H-1,2,3-TRIAZOL-4-YL]METHYL (1R,2R)-2-HYDROXY-2,3-DIHYDRO-1H-INDEN-1-YLCARBAMATE


Mass: 663.784 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H41N5O7S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 293 / 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: 2.93 Å3/Da / Density % sol: 58.08 %
Crystal growTemperature: 281.16 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 0.1M Na Acetate, 3.5 NaBr, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 281.16K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54178 Å
DetectorType: RIGAKU SATURN 92 / Detector: CCD / Date: Apr 1, 2006 / Details: Rigaku VariMax HF Confocal Mirror
RadiationMonochromator: Rigaku VariMax HF Confocal Mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.3→61.24 Å / Num. obs: 32061 / % possible obs: 92.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 3 / Redundancy: 1.67 % / Rmerge(I) obs: 0.039 / Χ2: 0.99 / Net I/σ(I): 10.1 / Scaling rejects: 724
Reflection shellResolution: 1.3→1.35 Å / Redundancy: 1.3 % / Rmerge(I) obs: 0.438 / Mean I/σ(I) obs: 1.6 / Num. measured all: 5963 / Num. unique all: 4581 / Χ2: 1.4 / % possible all: 74.1

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Phasing

Phasing MRRfactor: 0.545 / Cor.coef. Fo:Fc: 0.299
Highest resolutionLowest resolution
Rotation3 Å43.31 Å
Translation3 Å43.31 Å

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Processing

Software
NameVersionClassificationNB
d*TREK9.4SSIdata scaling
MOLREPphasing
SHELXrefinement
PDB_EXTRACT2data extraction
CrystalCleardata reduction
SHELXLrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.3→87 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.168 1137 Random
Rwork0.1416 --
all0.1612 23580 -
obs0.1938 22663 -
Displacement parametersBiso mean: 19.451 Å2
Refinement stepCycle: LAST / Resolution: 1.3→87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1510 0 59 293 1862
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg2.5

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