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- PDB-5vea: HIV Protease (PR) with TL-3 in active site and 4-methylbenzene-1,... -

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Basic information

Entry
Database: PDB / ID: 5vea
TitleHIV Protease (PR) with TL-3 in active site and 4-methylbenzene-1,2-diamine in exosite
ComponentsHIV-1 protease
KeywordsHYDROLASE / protease / allostery / fragment binding / exosite
Function / homology
Function and homology information


: / : / 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 ...: / : / 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 / RNA 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
N-[(benzyloxy)carbonyl]-L-alanyl-N-[(1R)-1-benzyl-2-oxoethyl]-L-valinamide / Chem-3TL / 4-methylbenzene-1,2-diamine / Gag-Pol polyprotein / Protease
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å
AuthorsStout, C.D.
CitationJournal: to be published
Title: Fragment-based campaign for the identification of potential exosite binders of HIV-1 Protease
Authors: Forli, S. / Tiefenbrunn, T. / Baksh, M.M. / Chang, M.W. / Perryman, A. / Garg, D. / Happer, M. / Lin, Y.-C. / Goodsell, D. / Angelina, E.L. / De Vera, I. / Kojetin, D. / Torbett, B.E. / ...Authors: Forli, S. / Tiefenbrunn, T. / Baksh, M.M. / Chang, M.W. / Perryman, A. / Garg, D. / Happer, M. / Lin, Y.-C. / Goodsell, D. / Angelina, E.L. / De Vera, I. / Kojetin, D. / Torbett, B.E. / Finn, M.G. / Elder, J. / Stout, C.D. / Olson, A.
History
DepositionApr 4, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 25, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HIV-1 protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,0976
Polymers10,8321
Non-polymers1,2665
Water84747
1
A: HIV-1 protease
hetero molecules

A: HIV-1 protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,19512
Polymers21,6642
Non-polymers2,53110
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z+1/31
Buried area6200 Å2
ΔGint-14 kcal/mol
Surface area9900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.763, 62.763, 82.238
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-205-

HOH

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Components

#1: Protein HIV-1 protease /


Mass: 10831.833 Da / Num. of mol.: 1 / Mutation: Q7K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Strain: R8 / Gene: pol / Plasmid: PET 21A+ / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21(DE3)
References: UniProt: Q72863, UniProt: P12497*PLUS, 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-9AY / 4-methylbenzene-1,2-diamine


Mass: 122.168 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H10N2
#4: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE / Dimethyl sulfoxide


Mass: 78.133 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 47 / 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: 2.16 Å3/Da / Density % sol: 43.01 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.8 / Details: 0.5M KSCN, 0.1 M MES-HCl pH 5.8, 10% DMSO

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 12, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2→32.793 Å / Num. obs: 6945 / % possible obs: 100 % / Redundancy: 9.4 % / Rmerge(I) obs: 0.097 / Rpim(I) all: 0.033 / Rrim(I) all: 0.103 / Rsym value: 0.097 / Net I/av σ(I): 5.1 / Net I/σ(I): 14.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsRpim(I) allRrim(I) allRsym value% possible all
2-2.059.80.6710.2260.7090.67100
2.05-2.119.70.5781.20.1950.6110.578100
2.11-2.179.80.4661.50.1560.4920.466100
2.17-2.249.70.34620.1140.3650.346100
2.24-2.319.70.3122.30.1040.3290.312100
2.31-2.399.60.3072.40.1030.3250.307100
2.39-2.489.60.262.70.0860.2740.26100
2.48-2.589.60.2073.30.0680.2180.207100
2.58-2.79.50.1743.80.0570.1840.174100
2.7-2.839.50.1464.10.0480.1540.146100
2.83-2.989.30.1244.90.0420.1310.124100
2.98-3.169.30.1045.90.0340.110.104100
3.16-3.389.30.0886.70.0290.0930.088100
3.38-3.659.10.0776.70.0270.0820.07799.9
3.65-48.80.0638.40.0220.0670.063100
4-4.478.50.04711.70.0170.0510.047100
4.47-5.168.40.04512.10.0160.0480.04599.7
5.16-6.328.90.04812.30.0160.050.048100
6.32-8.948.40.05690.0220.060.056100
8.94-41.1196.60.0627.40.0230.0660.06298.3

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation3 Å32.79 Å
Translation3 Å32.79 Å

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Processing

Software
NameVersionClassification
MOSFLMdata collection
SCALA3.2.25data scaling
MOLREP6data processing
REFMAC5.2.0019refinement
PDB_EXTRACT3.22data extraction
MOSFLMdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2AZ8

2az8


Resolution: 2→31.39 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.936 / SU B: 6.244 / SU ML: 0.172 / SU R Cruickshank DPI: 0.2317 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.232 / ESU R Free: 0.207 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2799 328 4.7 %RANDOM
Rwork0.2148 ---
obs0.2178 6578 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 80.66 Å2 / Biso mean: 33.439 Å2 / Biso min: 14.69 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20.01 Å20 Å2
2--0.02 Å20 Å2
3----0.03 Å2
Refinement stepCycle: final / Resolution: 2→31.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms759 0 54 47 860
Biso mean--44.96 41.8 -
Num. residues----99
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0270.021937
X-RAY DIFFRACTIONr_angle_refined_deg2.1951.9951434
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0617.5200
X-RAY DIFFRACTIONr_dihedral_angle_2_deg43.2524.64328
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.10315145
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.719154
X-RAY DIFFRACTIONr_chiral_restr0.1480.2129
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021018
X-RAY DIFFRACTIONr_nbd_refined0.2770.2359
X-RAY DIFFRACTIONr_nbtor_refined0.3190.2538
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.230.234
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3570.280
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2960.27
LS refinement shellResolution: 2.001→2.052 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.374 22 -
Rwork0.278 464 -
all-486 -
obs--100 %

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