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- PDB-2p3c: Crystal Structure of the subtype F wild type HIV protease complex... -

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Basic information

Entry
Database: PDB / ID: 2p3c
TitleCrystal Structure of the subtype F wild type HIV protease complexed with TL-3 inhibitor
Componentsprotease
KeywordsHYDROLASE/HYDROLASE INHIBITOR / wild type subtype F HIV protease / TL-3 inhibitor / non-B HIV protease / HYDROLASE-HYDROLASE INHIBITOR COMPLEX
Function / homology
Function and homology information


aspartic-type endopeptidase activity
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-[(benzyloxy)carbonyl]-L-alanyl-N-[(1R)-1-benzyl-2-oxoethyl]-L-valinamide / Chem-3TL / ACETIC ACID / Protease
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsSanches, M. / Krauchenco, S. / Martins, N.H. / Gustchina, A. / Wlodawer, A. / Polikarpov, I.
Citation
Journal: J.Mol.Biol. / Year: 2007
Title: Structural Characterization of B and non-B Subtypes of HIV-Protease: Insights into the Natural Susceptibility to Drug Resistance Development.
Authors: Sanches, M. / Krauchenco, S. / Martins, N.H. / Gustchina, A. / Wlodawer, A. / Polikarpov, I.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2004
Title: Crystallization of A non-B and a B mutant HIV protease
Authors: Sanches, M. / Martins, N.H. / Calazans, A. / Brindeiro, R.M. / Tanuri, A. / Antunes, O.A.C. / Polikarpov, I.
History
DepositionMar 8, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 24, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Structure summary / Version format compliance
Revision 1.3Jul 27, 2011Group: Other
Revision 1.4Feb 27, 2013Group: Other
Revision 1.5Oct 18, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software / Item: _software.name
Revision 1.6Oct 20, 2021Group: Advisory / Database references / Derived calculations
Category: database_2 / pdbx_unobs_or_zero_occ_atoms ...database_2 / pdbx_unobs_or_zero_occ_atoms / 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
Revision 1.7Apr 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: protease
B: protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,5716
Polymers21,4812
Non-polymers1,0894
Water2,108117
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4990 Å2
ΔGint-27 kcal/mol
Surface area9210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.425, 61.425, 80.892
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31A
41B
51A
61B

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PROPROGLUGLU1AA1 - 341 - 34
21PROPROGLUGLU1BB1 - 341 - 34
32ASPASPLEULEU2AA35 - 6435 - 64
42ASPASPLEULEU2BB35 - 6435 - 64
53GLUGLUPHEPHE1AA65 - 9965 - 99
63GLUGLUPHEPHE1BB65 - 9965 - 99

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Components

#1: Protein protease


Mass: 10740.737 Da / Num. of mol.: 2 / Mutation: Q7K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Genus: Lentivirus / Gene: pol / Plasmid: pET11a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q6Q004, HIV-1 retropepsin
#2: Chemical ChemComp-3TL / benzyl [(1S,4S,7S,8R,9R,10S,13S,16S)-7,10-dibenzyl-8,9-dihydroxy-1,16-dimethyl-4,13-bis(1-methylethyl)-2,5,12,15,18-pentaoxo-20-phenyl-19-oxa-3,6,11,14,17-pentaazaicos-1-yl]carbamate / TL-3, C2 symmetric inhibitor


Type: peptide-like, Peptide-like / Class: Inhibitor / Mass: 909.077 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C50H64N6O10
References: N-[(benzyloxy)carbonyl]-L-alanyl-N-[(1R)-1-benzyl-2-oxoethyl]-L-valinamide
#3: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H4O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 117 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsTHE INHIBITOR IS A C2 SYMMETRIC HIV PROTEASE

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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: 2.05 Å3/Da / Density % sol: 39.99 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: 0.8M ammonium sulfate, 0.1M sodium cacodylate. The crystals nucleated at 277K and were transfered to 291K for further growth. The protein to well proportion was 2:1, pH 6.2, VAPOR DIFFUSION, HANGING DROP

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: D03B-MX1 / Wavelength: 1.43
DetectorType: MAR CCD 165 mm / Detector: CCD
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SI 111 CHANNELSINGLE WAVELENGTHMx-ray1
2Mx-ray1
Radiation wavelengthWavelength: 1.43 Å / Relative weight: 1
ReflectionResolution: 2.1→53.225 Å / Num. obs: 10162 / % possible obs: 99.7 % / Redundancy: 2.5 % / Rmerge(I) obs: 0.046 / Rsym value: 0.046 / Net I/σ(I): 10.8
Reflection shell

Diffraction-ID: 1,2

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.1-2.212.40.3182.1363814910.31899.8
2.21-2.352.40.2342.8339813890.23499.8
2.35-2.512.40.1772.6319913070.177100
2.51-2.712.40.1145.9301812340.114100
2.71-2.972.50.0729.6278411310.072100
2.97-3.322.50.04713.7254310280.047100
3.32-3.832.50.03417.622709090.034100
3.83-4.72.50.02620.119157620.02699.7
4.7-6.642.50.02324.415165990.02399.1
6.64-32.212.60.02616.98003120.02694.2

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Processing

Software
NameVersionClassificationNB
SCALAdata scaling
REFMAC5.2.0003refinement
PDB_EXTRACT2data extraction
MAR345345DTBdata collection
MOSFLMdata reduction
CCP4(SCALA)data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Crystal Structure of the multi-drug resistant mutant subtype B HIV protease complexed with TL-3 inhibitor

Resolution: 2.1→25.27 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.925 / SU B: 14.02 / SU ML: 0.202 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.262 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.265 1008 10 %RANDOM
Rwork0.194 ---
obs0.201 10121 99.67 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.515 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å2-0.01 Å20 Å2
2---0.01 Å20 Å2
3---0.02 Å2
Refinement stepCycle: LAST / Resolution: 2.1→25.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1504 0 78 117 1699
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0221806
X-RAY DIFFRACTIONr_angle_refined_deg1.5932.0632450
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.075220
X-RAY DIFFRACTIONr_dihedral_angle_2_deg44.81425.18554
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.90915309
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.096156
X-RAY DIFFRACTIONr_chiral_restr0.0860.2277
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021328
X-RAY DIFFRACTIONr_nbd_refined0.2310.21042
X-RAY DIFFRACTIONr_nbtor_refined0.3220.21196
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2010.2156
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2430.279
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1310.24
X-RAY DIFFRACTIONr_mcbond_it1.5461.51092
X-RAY DIFFRACTIONr_mcangle_it2.74921741
X-RAY DIFFRACTIONr_scbond_it2.3913792
X-RAY DIFFRACTIONr_scangle_it3.3334.5709
X-RAY DIFFRACTIONr_rigid_bond_restr1.68931729
X-RAY DIFFRACTIONr_sphericity_bonded14.49931620
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
663TIGHT POSITIONAL0.030.05
111MEDIUM POSITIONAL0.310.5
663TIGHT THERMAL0.170.5
111MEDIUM THERMAL0.52
LS refinement shellResolution: 2.101→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.382 74 -
Rwork0.274 672 -
obs-746 99.73 %

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