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- PDB-4k4q: TL-3 inhibited Trp6Ala HIV Protease with 3-bromo-2,6-dimethoxyben... -

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Basic information

Entry
Database: PDB / ID: 4k4q
TitleTL-3 inhibited Trp6Ala HIV Protease with 3-bromo-2,6-dimethoxybenzoic acid bound in flap site
ComponentsHIV-1 protease
KeywordsHYDROLASE/HYDROLASE INHIBITOR / fragment binding / exosite / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / host multivesicular body / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency ...HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / host multivesicular body / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / symbiont-mediated suppression of host gene expression / viral penetration into host nucleus / RNA stem-loop binding / RNA-directed DNA polymerase activity / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / host cell / viral nucleocapsid / DNA recombination / DNA-directed DNA polymerase / Hydrolases; Acting on ester bonds / aspartic-type endopeptidase activity / DNA-directed DNA polymerase activity / symbiont entry into host cell / viral translational frameshifting / lipid binding / host cell nucleus / host cell plasma membrane / structural molecule activity / virion membrane / 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. / Retropepsin-like catalytic domain / RNase H type-1 domain profile. / Ribonuclease H domain / Matrix protein, lentiviral and alpha-retroviral, N-terminal / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / Reverse transcriptase domain / Reverse transcriptase (RT) catalytic domain profile. / Retropepsins / Retroviral aspartyl protease / Aspartyl protease, retroviral-type family profile. / Peptidase A2A, retrovirus, catalytic / Reverse transcriptase (RNA-dependent DNA polymerase) / Retroviral matrix protein / Retrovirus capsid, C-terminal / 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
N-[(benzyloxy)carbonyl]-L-alanyl-N-[(1R)-1-benzyl-2-oxoethyl]-L-valinamide / 3-bromo-2,6-dimethoxybenzoic acid / Chem-3TL / BETA-MERCAPTOETHANOL / NITRATE ION / Gag-Pol polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 Å
AuthorsTiefenbrunn, T. / Stout, C.D.
CitationJournal: Chem.Biol.Drug Des. / Year: 2014
Title: Crystallographic Fragment-Based Drug Discovery: Use of a Brominated Fragment Library Targeting HIV Protease.
Authors: Tiefenbrunn, T. / Forli, S. / Happer, M. / Gonzalez, A. / Tsai, Y. / Soltis, M. / Elder, J.H. / Olson, A.J. / Stout, C.D.
History
DepositionApr 12, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 18, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 12, 2014Group: Database references
Revision 1.2Feb 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: HIV-1 protease
B: HIV-1 protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,73215
Polymers21,4332
Non-polymers2,29913
Water1,40578
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6760 Å2
ΔGint-25 kcal/mol
Surface area9520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.818, 97.818, 98.777
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number98
Space group name H-MI4122
Components on special symmetry positions
IDModelComponents
11A-207-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein HIV-1 protease


Mass: 10716.701 Da / Num. of mol.: 2 / Mutation: W6A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: gag-pol / Plasmid: pET-21a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2(DE3) pLysS / References: UniProt: P12499, HIV-1 retropepsin

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Non-polymers , 6 types, 91 molecules

#2: Chemical
ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: NO3
#3: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS
#4: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: 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
#6: Chemical ChemComp-06B / 3-bromo-2,6-dimethoxybenzoic acid


Mass: 261.069 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C9H9BrO4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 78 / 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: 2.76 Å3/Da / Density % sol: 55.37 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 5
Details: 0.1M NaOAc pH 5.0, 2.5M NaNO3, vapor diffusion, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.918 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Mar 23, 2012 / Details: Rh Coated flat mirror
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 1.8→39.986 Å / Num. all: 11388 / Num. obs: 11388 / % possible obs: 99 % / Redundancy: 6.6 % / Rsym value: 0.053 / Net I/σ(I): 22
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.26-2.3850.2642.7765615430.26494.1
2.38-2.5270.223.21091015600.2299.8
2.52-2.770.1594.51024414610.15999.9
2.7-2.917.10.1056.7973913790.10599.9
2.91-3.197.10.06410.5896612680.06499.9
3.19-3.576.80.04912.5786611530.04999.9
3.57-4.126.80.03915.5698610300.03999.9
4.12-5.046.90.03416.760778810.03499.9
5.04-7.136.50.03515.945977020.03599.9
7.13-39.9866.10.04212.525094110.04298.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALA3.3.16data scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
Blu-Icedata collection
autoXDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→34.58 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.951 / WRfactor Rfree: 0.2197 / WRfactor Rwork: 0.1871 / Occupancy max: 1 / Occupancy min: 0.35 / FOM work R set: 0.8553 / SU B: 4.878 / SU ML: 0.08 / SU R Cruickshank DPI: 0.124 / SU Rfree: 0.12 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.124 / ESU R Free: 0.12 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2297 1138 5.1 %RANDOM
Rwork0.1953 ---
obs0.197 -99.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 88.56 Å2 / Biso mean: 32.1637 Å2 / Biso min: 19.27 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å20 Å2-0 Å2
2---0.02 Å20 Å2
3---0.04 Å2
Refinement stepCycle: LAST / Resolution: 1.8→34.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1486 0 144 78 1708
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0191645
X-RAY DIFFRACTIONr_bond_other_d0.0010.021669
X-RAY DIFFRACTIONr_angle_refined_deg1.4022.0762216
X-RAY DIFFRACTIONr_angle_other_deg0.87733820
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2275196
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.44425.09851
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.43215277
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.715158
X-RAY DIFFRACTIONr_chiral_restr0.070.2258
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0211729
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02303
X-RAY DIFFRACTIONr_mcbond_it0.9312.021791
X-RAY DIFFRACTIONr_mcbond_other0.9152.017789
X-RAY DIFFRACTIONr_mcangle_it1.4513.018984
LS refinement shellResolution: 1.803→1.85 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.302 80 -
Rwork0.268 1480 -
all-1560 -
obs--96.36 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.18120.3945-0.620.4114-0.26360.6483-0.128-0.0412-0.27870.05530.0561-0.12640.1187-0.03590.07190.12560.0108-0.00790.0758-0.00140.0521-7.135-24.12132.452
21.23110.2736-0.0971.4504-0.4291.7713-0.00180.1010.0564-0.04110.0394-0.3183-0.16730.1786-0.03760.038-0.01770.0060.0817-0.02770.11175.572-9.87320.91
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 99
2X-RAY DIFFRACTION2B1 - 99

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