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- PDB-4ll3: Structure of wild-type HIV protease in complex with darunavir -

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Basic information

Entry
Database: PDB / ID: 4ll3
TitleStructure of wild-type HIV protease in complex with darunavir
ComponentsProtease
KeywordsHydrolase/Hydrolase Inhibitor / Hydrolase Inhibitor-darunavir / Hydrolase-Hydrolase Inhibitor complex / HIV-1 protease / TMC114
Function / homology
Function and homology information


pepsin A / viral genome integration into host DNA / establishment of integrated proviral latency / RNA-directed DNA polymerase activity / endonuclease activity / aspartic-type endopeptidase activity / proteolysis / DNA binding / zinc ion binding
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 / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase domain ...: / 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 / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase domain / Reverse transcriptase (RT) catalytic domain profile. / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Aspartic peptidase domain superfamily / Reverse transcriptase/Diguanylate cyclase domain / DNA/RNA polymerase superfamily / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsGrantz Saskova, K. / Rezacova, P. / Brynda, J. / Kozisek, M. / Konvalinka, J.
CitationJournal: Febs J. / Year: 2014
Title: Thermodynamic and structural analysis of HIV protease resistance to darunavir - analysis of heavily mutated patient-derived HIV-1 proteases.
Authors: Kozisek, M. / Lepsik, M. / Grantz Saskova, K. / Brynda, J. / Konvalinka, J. / Rezacova, P.
History
DepositionJul 9, 2013Deposition site: RCSB / Processing site: RCSB
SupersessionApr 16, 2014ID: 3QOZ
Revision 1.0Apr 16, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 24, 2014Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / struct_ncs_dom_lim / struct_site
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_alt_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_alt_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,7574
Polymers21,6622
Non-polymers1,0952
Water2,540141
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5760 Å2
ΔGint-39 kcal/mol
Surface area9310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.557, 62.557, 81.523
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 (eV)
11A
21B
12A
22B

NCS domain segments:

Component-ID: 1 / Refine code: 3

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-IDBeg label alt-IDEnd label alt-ID
11PROPROPHEPHEAA1 - 991 - 99
21PROPROPHEPHEBB1 - 991 - 99
1217171717AC201AA
2217171717AD202BB

NCS ensembles :
ID
1
2

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Components

#1: Protein Protease


Mass: 10830.781 Da / Num. of mol.: 2 / Fragment: UNP residues 7-105
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / References: UniProt: Q9WFL7
#2: Chemical ChemComp-017 / (3R,3AS,6AR)-HEXAHYDROFURO[2,3-B]FURAN-3-YL(1S,2R)-3-[[(4-AMINOPHENYL)SULFONYL](ISOBUTYL)AMINO]-1-BENZYL-2-HYDROXYPROPYLCARBAMATE / Darunavir / TMC114 / UIC-94017


Mass: 547.664 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H37N3O7S / Comment: medication, antiretroviral*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 141 / 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: 41.99 %
Crystal growDetails: RESERVOIR: 2 M SODIUM FORMATE, 0.1 M SODIUM ACETATE, PH 4.6. DROPS: 2 UL PROTEIN + 1UL RESERVOIR, PROTEIN CONCENTRATION 5MG/ML, 5-FOLD MOLAR EXCESS OF INHIBITOR (DISSOLVED IN DMSO) OVER ...Details: RESERVOIR: 2 M SODIUM FORMATE, 0.1 M SODIUM ACETATE, PH 4.6. DROPS: 2 UL PROTEIN + 1UL RESERVOIR, PROTEIN CONCENTRATION 5MG/ML, 5-FOLD MOLAR EXCESS OF INHIBITOR (DISSOLVED IN DMSO) OVER PROTEIN, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X12 / Wavelength: 0.953
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 27, 2009
RadiationMonochromator: DOUBLE CRYSTAL SI(111), HORIZONTALLY FOCUSSING
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. obs: 13257 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 6.7 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 26.45
Reflection shellResolution: 1.95→2.02 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.513 / Mean I/σ(I) obs: 2.7 / % possible all: 99.9

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Processing

Software
NameVersionClassification
MOLREPphasing
REFMAC5.2.0019refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→27.09 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.946 / SU B: 9.638 / SU ML: 0.145 / Cross valid method: THROUGHOUT / ESU R: 0.21 / ESU R Free: 0.173 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23 662 5 %RANDOM
Rwork0.18288 ---
obs0.18523 12558 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.773 Å2
Baniso -1Baniso -2Baniso -3
1--0.23 Å2-0.11 Å20 Å2
2---0.23 Å20 Å2
3---0.34 Å2
Refinement stepCycle: LAST / Resolution: 1.95→27.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1520 0 76 141 1737
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0221696
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5082.0342318
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3325212
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.98125.08261
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.07915295
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.813158
X-RAY DIFFRACTIONr_chiral_restr0.10.2277
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021226
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2090.2763
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3140.21146
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1710.2147
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2330.249
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1340.24
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2961.51057
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.30121657
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.9083735
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.0844.5657
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

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

Ens-IDNumberTypeRms dev position (Å)Weight position
1394tight positional0.020.05
1371loose positional0.745
238loose positional0.045
1394tight thermal0.320.5
1371loose thermal0.9410
238loose thermal1.0510
LS refinement shellResolution: 1.95→2.001 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.37 50 -
Rwork0.256 907 -
obs--99.69 %

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