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- PDB-4mc6: HIV protease in complex with SA499 -

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Basic information

Entry
Database: PDB / ID: 4mc6
TitleHIV protease in complex with SA499
ComponentsProtease
KeywordsHYDROLASE/HYDROLASE INHIBITOR / carbamates / drug design / HIV protease inhibitors / protein binding / stereoisomerism / structure-activity relationship / thiazepines / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


RNA stem-loop binding / host cell / HIV-1 retropepsin / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / host multivesicular body / DNA integration / RNA-directed DNA polymerase / viral genome integration into host DNA ...RNA stem-loop binding / host cell / HIV-1 retropepsin / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / host multivesicular body / DNA integration / RNA-directed DNA polymerase / viral genome integration into host DNA / viral penetration into host nucleus / establishment of integrated proviral latency / RNA-directed DNA polymerase activity / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / symbiont-mediated suppression of host gene expression / viral nucleocapsid / DNA recombination / Hydrolases; Acting on ester bonds / DNA-directed DNA polymerase / aspartic-type endopeptidase activity / DNA-directed DNA polymerase activity / symbiont entry into host cell / lipid binding / host cell nucleus / host cell plasma membrane / virion membrane / structural molecule activity / 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 / Zinc finger, CCHC-type superfamily / Cathepsin D, subunit A; domain 1 / Acid Proteases / 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
Chem-23K / Gag-Pol polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.31 Å
AuthorsGanguly, A.K. / Alluri, S.S. / Wang, C. / Antropow, A. / White, A. / Caroccia, D. / Biswas, D. / Kang, E. / Zhang, L. / Carroll, S.S. ...Ganguly, A.K. / Alluri, S.S. / Wang, C. / Antropow, A. / White, A. / Caroccia, D. / Biswas, D. / Kang, E. / Zhang, L. / Carroll, S.S. / Burlein, C. / Munshi, V. / Orth, P. / Strickland, C.
CitationJournal: Tetrahedron / Year: 2014
Title: Structural Optimization of Cyclic Sulfonamide based Novel HIV-1 Protease Inhibitors to Pico Molar Affinities guided by X-ray Crystallographic Analysis
Authors: Ganguly, A.K. / Alluri, S.S. / Wang, C.H. / Antropow, A. / White, A. / Caroccia, D. / Biswas, D. / Kang, E. / Zhang, L.K. / Carroll, S.S. / Burlein, C. / Fay, J. / Orth, P. / Strickland, C.
History
DepositionAug 21, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 2, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_ref_seq_dif.details / _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)22,2987
Polymers21,6102
Non-polymers6885
Water4,972276
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4490 Å2
ΔGint-46 kcal/mol
Surface area9420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.980, 85.860, 46.280
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Protease / / PR / Retropepsin


Mass: 10804.808 Da / Num. of mol.: 2 / Fragment: UNP residues 489-587 / Mutation: Q7K V32I L63I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: gag-pol / Production host: Escherichia coli (E. coli) / References: UniProt: P0C6F2, HIV-1 retropepsin
#2: Chemical ChemComp-23K / 1-tert-butyl-3-{(2S,3R)-4-[(4R)-7-fluoro-1,1-dioxido-4-(propan-2-yl)-4,5-dihydro-1,2-benzothiazepin-2(3H)-yl]-3-hydroxy-1-phenylbutan-2-yl}urea


Mass: 519.672 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H38FN3O4S
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 276 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.71 Å3/Da / Density % sol: 54.63 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 0.7 M sodium chloride, 100 mM sodium citrate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 23, 2013
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.31→85.86 Å / Num. all: 56710 / Num. obs: 56540 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 14.26 Å2
Reflection shellHighest resolution: 1.31 Å

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Processing

Software
NameVersionClassification
CrystalCleardata collection
AMoREphasing
BUSTER2.11.1refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.31→46.28 Å / Cor.coef. Fo:Fc: 0.9571 / Cor.coef. Fo:Fc free: 0.96 / SU R Cruickshank DPI: 0.046 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.05 / SU Rfree Blow DPI: 0.05 / SU Rfree Cruickshank DPI: 0.047 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.1975 1192 2.11 %RANDOM
Rwork0.1806 ---
obs0.181 56491 98.67 %-
all-56710 --
Displacement parametersBiso mean: 17.71 Å2
Baniso -1Baniso -2Baniso -3
1--3.0831 Å20 Å20 Å2
2--1.1937 Å20 Å2
3---1.8893 Å2
Refine analyzeLuzzati coordinate error obs: 0.15 Å
Refinement stepCycle: LAST / Resolution: 1.31→46.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1504 0 43 276 1823
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.011640HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.222239HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d574SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes35HARMONIC2
X-RAY DIFFRACTIONt_gen_planes243HARMONIC5
X-RAY DIFFRACTIONt_it1640HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion4.29
X-RAY DIFFRACTIONt_other_torsion13.67
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion223SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact2118SEMIHARMONIC4
LS refinement shellResolution: 1.31→1.34 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2109 69 1.94 %
Rwork0.242 3491 -
all0.2413 3560 -
obs--98.67 %

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