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- PDB-3ia9: Crystal structure of a chemically synthesized [D25N]HIV-1 proteas... -

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Basic information

Entry
Database: PDB / ID: 3ia9
TitleCrystal structure of a chemically synthesized [D25N]HIV-1 protease molecule complexed with MVT-101 reduced isostere inhibitor
Components[D25N]HIV-1 protease
KeywordsHYDROLASE/HYDROLASE INHIBITOR / beta-sheet / 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
N-{(2S)-2-[(N-acetyl-L-threonyl-L-isoleucyl)amino]hexyl}-L-norleucyl-L-glutaminyl-N~5~-[amino(iminio)methyl]-L-ornithinamide / Chem-2NC / Protease
Similarity search - Component
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsTorbeev, V.Y. / Kent, S.B.H.
CitationJournal: To be Published
Title: Hydrogen bonds at the protein-inhibitor interface in the HIV-1 protease / inhibitors complexes probed by total chemical synthesis and X-ray crystallography
Authors: Torbeev, V.Y. / Kent, S.B.H.
History
DepositionJul 13, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 27, 2011Provider: repository / Type: Initial release
Revision 1.1Dec 12, 2012Group: Other

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: [D25N]HIV-1 protease
B: [D25N]HIV-1 protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,4825
Polymers21,5192
Non-polymers9633
Water2,216123
1
A: [D25N]HIV-1 protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,7234
Polymers10,7601
Non-polymers9633
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: [D25N]HIV-1 protease


Theoretical massNumber of molelcules
Total (without water)10,7601
Polymers10,7601
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4400 Å2
ΔGint-54 kcal/mol
Surface area9600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.090, 57.697, 61.832
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein [D25N]HIV-1 protease


Mass: 10759.640 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: total chemical synthesis / References: UniProt: O38732*PLUS, HIV-1 retropepsin
#2: Chemical ChemComp-2NC / N-{(2S)-2-[(N-acetyl-L-threonyl-L-isoleucyl)amino]hexyl}-L-norleucyl-L-glutaminyl-N~5~-[amino(iminio)methyl]-L-ornithinamide / p2/NC


Type: peptide-like, Peptide-like / Class: Inhibitor / Mass: 770.983 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C35H68N11O8
References: N-{(2S)-2-[(N-acetyl-L-threonyl-L-isoleucyl)amino]hexyl}-L-norleucyl-L-glutaminyl-N~5~-[amino(iminio)methyl]-L-ornithinamide
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 123 / 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: 2.12 Å3/Da / Density % sol: 41.91 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.1 M citrate, 0.2M sodium phosphate, 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: 21-ID-D / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 4, 2008
RadiationMonochromator: Fast monochromatic rotary beam shutters with opening and closing times less than 5 msec, synchronized, precisely with the motion state of the crystallographic spindle
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.3→50 Å / Num. obs: 45790 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.9 % / Rmerge(I) obs: 0.055 / Net I/σ(I): 32.97
Reflection shellResolution: 1.3→1.35 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.375 / Mean I/σ(I) obs: 3.36 / Num. unique all: 4507 / % possible all: 98.6

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.3→20 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.955 / SU B: 1.541 / SU ML: 0.032 / Cross valid method: THROUGHOUT / ESU R: 0.06 / ESU R Free: 0.056 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20786 2303 5.1 %RANDOM
Rwork0.17801 ---
obs0.1795 43280 99.44 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 12.869 Å2
Baniso -1Baniso -2Baniso -3
1--0.19 Å20 Å20 Å2
2--0.06 Å20 Å2
3---0.13 Å2
Refinement stepCycle: LAST / Resolution: 1.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1518 0 64 123 1705
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0221697
X-RAY DIFFRACTIONr_bond_other_d0.0020.021142
X-RAY DIFFRACTIONr_angle_refined_deg1.6971.9982281
X-RAY DIFFRACTIONr_angle_other_deg0.93532812
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6685208
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.07724.66760
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.17215301
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3271510
X-RAY DIFFRACTIONr_chiral_restr0.1040.2268
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021776
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02288
X-RAY DIFFRACTIONr_nbd_refined0.1980.2260
X-RAY DIFFRACTIONr_nbd_other0.2060.21146
X-RAY DIFFRACTIONr_nbtor_refined0.1770.2792
X-RAY DIFFRACTIONr_nbtor_other0.0890.2925
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1390.266
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0940.27
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1830.239
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1210.27
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.7831.51098
X-RAY DIFFRACTIONr_mcbond_other1.1051.5449
X-RAY DIFFRACTIONr_mcangle_it2.46421719
X-RAY DIFFRACTIONr_scbond_it4.0693673
X-RAY DIFFRACTIONr_scangle_it4.8264.5562
X-RAY DIFFRACTIONr_rigid_bond_restr3.35131763
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded4.62331661
LS refinement shellResolution: 1.298→1.332 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.254 163 -
Rwork0.198 3061 -
obs--97.23 %

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