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- PDB-3dck: X-ray structure of D25N chemical analogue of HIV-1 protease compl... -

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Basic information

Entry
Database: PDB / ID: 3dck
TitleX-ray structure of D25N chemical analogue of HIV-1 protease complexed with ketomethylene isostere inhibitor
ComponentsChemical analogue HIV-1 protease
KeywordsHYDROLASE/HYDROLASE INHIBITOR / HIV-1 protease / homodimer / beta-turns / beta-strand / HYDROLASE / HYDROLASE-HYDROLASE 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
(2S)-2-{[(2R,5S)-5-{[(2S,3S)-2-{[(2S,3R)-2-(ACETYLAMINO)-3-HYDROXYBUTANOYL]AMINO}-3-METHYLPENTANOYL]AMINO}-2-BUTYL-4-OXONONANOYL]AMINO}-N~1~-[(2S)-1-AMINO-5-CARBAMIMIDAMIDO-1-OXOPENTAN-2-YL]PENTANEDIAMIDE / Chem-KVI / Protease
Similarity search - Component
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsTorbeev, V.Y. / Mandal, K. / Terechko, V.A. / Kent, S.B.H.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2008
Title: Crystal structure of chemically synthesized HIV-1 protease and a ketomethylene isostere inhibitor based on the p2/NC cleavage site
Authors: Torbeev, V.Y. / Mandal, K. / Terechko, V.A. / Kent, S.B.H.
History
DepositionJun 3, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 19, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 16, 2013Group: Non-polymer description
Revision 1.3Oct 25, 2017Group: Refinement description / Category: software
Revision 1.4Nov 1, 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_sheet / 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_sheet.number_strands / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.6Mar 20, 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: Chemical analogue HIV-1 protease
B: Chemical analogue HIV-1 protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,3023
Polymers21,5192
Non-polymers7831
Water1,49583
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4080 Å2
ΔGint-22 kcal/mol
Surface area9550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.028, 58.551, 61.584
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Chemical analogue HIV-1 protease


Mass: 10759.640 Da / Num. of mol.: 2 / Fragment: HIV-1 protease / Mutation: D25N / Source method: obtained synthetically
Details: total chemical protein synthesis using solid phase peptide synthesis and native chemical ligation
References: UniProt: O38732*PLUS, HIV-1 retropepsin
#2: Chemical ChemComp-KVI / (2S)-2-{[(2R,5S)-5-{[(2S,3S)-2-{[(2S,3R)-2-(acetylamino)-3-hydroxybutanoyl]amino}-3-methylpentanoyl]amino}-2-butyl-4-oxononanoyl]amino}-N~1~-[(2S)-1-amino-5-carbamimidamido-1-oxopentan-2-yl]pentanediamide


Type: peptide-like, Peptide-like / Class: Inhibitor / Mass: 782.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C36H66N10O9 / Details: The peptide inhibitor was chemically synthesized
References: (2S)-2-{[(2R,5S)-5-{[(2S,3S)-2-{[(2S,3R)-2-(ACETYLAMINO)-3-HYDROXYBUTANOYL]AMINO}-3-METHYLPENTANOYL]AMINO}-2-BUTYL-4-OXONONANOYL]AMINO}-N~1~-[(2S)-1-AMINO-5-CARBAMIMIDAMIDO-1-OXOPENTAN-2-YL]PENTANEDIAMIDE
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 83 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsSEQUENCE OF ENTITY 1 WAS BASED ON UNP DB CODE POL_HV1A2, ACCESSION P03369, RESIDUES 491-589. D25N ...SEQUENCE OF ENTITY 1 WAS BASED ON UNP DB CODE POL_HV1A2, ACCESSION P03369, RESIDUES 491-589. D25N OF THE SEQUENCE WAS A DESIGNED MUTATION TO THE DATABASE.

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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: 2.07 Å3/Da / Density % sol: 40.47 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.1M CITRATE, 0.2M SODIUM PHOPHATE, 30% (W/V) AMMONIUM SULFATE, 10% (V/V) DMSO, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.97934 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 7, 2007
Details: Si(111) Double Crystal Monochrometer. Adjustable focusing mirrors in K-B geometry
RadiationMonochromator: Double crystal cryo-cooled Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. all: 17570 / Num. obs: 17428 / % possible obs: 99.2 % / Observed criterion σ(I): 7.8 / Redundancy: 7.8 % / Rmerge(I) obs: 0.089 / Rsym value: 0.07 / Net I/σ(I): 31.3
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 7.9 % / Rmerge(I) obs: 0.59 / Mean I/σ(I) obs: 3.9 / Num. unique all: 1708 / Rsym value: 0.495 / % possible all: 98.6

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.2.0019refinement
PDB_EXTRACT3.005data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4HVP

4hvp


Resolution: 1.8→20 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.946 / SU B: 5.356 / SU ML: 0.082 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.147 / ESU R Free: 0.13 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.223 882 5.1 %RANDOM
Rwork0.194 ---
obs0.196 17373 98.61 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.053 Å2
Baniso -1Baniso -2Baniso -3
1--1.47 Å20 Å20 Å2
2--1.78 Å20 Å2
3----0.32 Å2
Refinement stepCycle: LAST / Resolution: 1.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1518 0 55 83 1656
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0221597
X-RAY DIFFRACTIONr_angle_refined_deg1.5951.9962158
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9545197
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.58425.08857
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.15315283
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.4158
X-RAY DIFFRACTIONr_chiral_restr0.1180.2254
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021132
X-RAY DIFFRACTIONr_nbd_refined0.2570.2662
X-RAY DIFFRACTIONr_nbtor_refined0.3140.21060
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1630.280
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1730.234
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1870.23
X-RAY DIFFRACTIONr_mcbond_it1.0481.51035
X-RAY DIFFRACTIONr_mcangle_it1.64821633
X-RAY DIFFRACTIONr_scbond_it2.5143633
X-RAY DIFFRACTIONr_scangle_it4.1854.5525
LS refinement shellResolution: 1.801→1.848 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.31 72 -
Rwork0.216 1057 -
all-1129 -
obs--89.25 %
Refinement TLS params.Method: refined / Origin x: -4.9432 Å / Origin y: 1.2977 Å / Origin z: -18.2686 Å
111213212223313233
T-0.0597 Å20.002 Å20.007 Å2--0.0572 Å2-0.0167 Å2---0.0993 Å2
L2.7081 °20.6246 °20.3881 °2-1.6055 °2-0.6418 °2--1.2452 °2
S-0.0314 Å °-0.0809 Å °-0.0327 Å °-0.0023 Å °0.0786 Å °-0.026 Å °0.0011 Å °-0.1348 Å °-0.0472 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 991 - 99
2X-RAY DIFFRACTION1BC1010 - 5
3X-RAY DIFFRACTION1BB1 - 991 - 99

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