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- PDB-1sp5: Crystal structure of HIV-1 protease complexed with a product of a... -

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Basic information

Entry
Database: PDB / ID: 1sp5
TitleCrystal structure of HIV-1 protease complexed with a product of autoproteolysis
Components
  • 5-mer peptide from Protease
  • Protease
KeywordsHYDROLASE / product / autoproteolysis / self-digestion / autodigestion / aspartic protease / HIV / protease / complex(aspartic protease-peptide)
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 / establishment of integrated proviral latency / viral penetration into host nucleus ...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 / establishment of integrated proviral latency / viral penetration into host nucleus / 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 / structural molecule activity / virion membrane / 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 / Cathepsin D, subunit A; domain 1 / Acid Proteases / 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. / 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
BETA-MERCAPTOETHANOL / Gag-Pol polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.8 Å
AuthorsVondrackova, E. / Hasek, J. / Jaskolski, M. / Rezacova, P. / Dohnalek, J. / Skalova, T. / Petrokova, H. / Duskova, J. / Brynda, J. / Sedlacek, J.
CitationJournal: To be Published
Title: Product of enzymatic self-cleavage bound in the active site of HIV protease
Authors: Vondrackova, E. / Hasek, J. / Jaskolski, M. / Rezacova, P. / Dohnalek, J. / Skalova, T. / Petrokova, H. / Duskova, J. / Brynda, J. / Sedlacek, J.
History
DepositionMar 16, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 19, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / 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_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protease
B: Protease
I: 5-mer peptide from Protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,67710
Polymers22,2583
Non-polymers4197
Water2,432135
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5810 Å2
ΔGint-60 kcal/mol
Surface area9370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.765, 86.284, 45.834
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
DetailsThe biological assembly corresponds to the contents of asymmetric unit (HIV protease dimer).

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Components

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Protein / Protein/peptide , 2 types, 3 molecules ABI

#1: Protein Protease / Retropepsin / POL polyprotein


Mass: 10803.756 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Genus: Lentivirus / Gene: POL / Plasmid: pT7Q10H1N / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P03367, HIV-1 retropepsin
#2: Protein/peptide 5-mer peptide from Protease / Autoproteolytic Product Containing Tyr-Asp-Gln-Ile-Leu Sequence


Mass: 650.721 Da / Num. of mol.: 1 / Fragment: Residues 59-63
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Genus: Lentivirus / Gene: POL / Plasmid: pT7Q10H1N / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P03367

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Non-polymers , 4 types, 142 molecules

#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6OS
#5: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 135 / 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: 2.37 Å3/Da / Density % sol: 47.7 %
Crystal growTemperature: 279 K / Method: vapor diffusion, hanging drop / pH: 5
Details: sodium chloride 0.8-0.9M, sodium citrate 50mM, DMSO 5%, sodium acetate 5mM, EDTA 0.5mM, DTT 0.25mM, Boc-Phe-psi[(S)-CH(OH)CH2NH]Phe-Ile-Phe-NH2 270mM, protein 3mg/ml in drop, pH 5.0, VAPOR ...Details: sodium chloride 0.8-0.9M, sodium citrate 50mM, DMSO 5%, sodium acetate 5mM, EDTA 0.5mM, DTT 0.25mM, Boc-Phe-psi[(S)-CH(OH)CH2NH]Phe-Ile-Phe-NH2 270mM, protein 3mg/ml in drop, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 279K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 16, 2000
RadiationMonochromator: double Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.801→25 Å / Num. all: 21152 / Num. obs: 21152 / % possible obs: 96.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.3 % / Biso Wilson estimate: 14 Å2 / Rmerge(I) obs: 0.049 / Rsym value: 0.049 / Net I/σ(I): 30.8
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.232 / Mean I/σ(I) obs: 7 / Num. unique all: 988 / Rsym value: 0.232 / % possible all: 92.9

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
CNS1.1phasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 1A30

1a30


Resolution: 1.8→19.1 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 1327403.76 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: MAXIMUM LIKELIHOOD USED DURING REFINEMENT, STANDARD CRYSTALLOGRAPHIC RESIDUAL IN THE LAST CYCLE WITH ALL REFLECTIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.211 1023 4.8 %RANDOM
Rwork0.177 ---
all0.178 21129 --
obs0.178 21129 96.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 74.8561 Å2 / ksol: 0.455801 e/Å3
Displacement parametersBiso mean: 15.9 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.21 Å0.17 Å
Luzzati d res low-5 Å
Luzzati sigma a0.1 Å0.12 Å
Refinement stepCycle: LAST / Resolution: 1.8→19.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1567 0 19 135 1721
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.013
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_deg1.6
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d26.2
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.92
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.551.5
X-RAY DIFFRACTIONc_mcangle_it2.332
X-RAY DIFFRACTIONc_scbond_it3.032
X-RAY DIFFRACTIONc_scangle_it4.572.5
LS refinement shellResolution: 1.8→1.87 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.237 97 4.8 %
Rwork0.207 1933 -
obs-2030 95.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_CME_REP.PARAMPROTEIN_CME.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
X-RAY DIFFRACTION4DMS.PARAMDMS.TOP

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