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- PDB-3kf0: HIV Protease with fragment 4D9 bound -

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Basic information

Entry
Database: PDB / ID: 3kf0
TitleHIV Protease with fragment 4D9 bound
ComponentsProtease
KeywordsHYDROLASE/HYDROLASE INHIBITOR / Protease / TL-3 inhibitor / fragment hit / Aspartyl protease / 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 / telomerase activity / viral penetration into host nucleus / RNA stem-loop binding / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / host cell / viral nucleocapsid / DNA recombination / DNA-directed DNA polymerase / aspartic-type endopeptidase activity / Hydrolases; Acting on ester bonds / DNA-directed DNA polymerase activity / symbiont-mediated suppression of host gene expression / symbiont entry into host cell / viral translational frameshifting / 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. / Retropepsin-like catalytic domain / Matrix protein, lentiviral and alpha-retroviral, N-terminal / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / RNase H type-1 domain profile. / Ribonuclease H domain / Retropepsins / Retroviral aspartyl protease / Aspartyl protease, retroviral-type family profile. / Peptidase A2A, retrovirus, catalytic / Reverse transcriptase domain / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase (RT) catalytic domain profile. / Retrovirus capsid, C-terminal / Retroviral matrix protein / Cathepsin D, subunit A; domain 1 / Acid Proteases / Retrovirus capsid, N-terminal / zinc finger / Zinc knuckle / Zinc finger, CCHC-type superfamily / Zinc finger, CCHC-type / Zinc finger CCHC-type profile. / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Aspartic peptidase domain superfamily / Ribonuclease H 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 / (1S,2S)-2-methylcyclohexanol / BETA-MERCAPTOETHANOL / : / Gag-Pol polyprotein / Protease
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsStout, C.D. / Perryman, A.L.
CitationJournal: Chem.Biol.Drug Des. / Year: 2010
Title: Fragment-based screen against HIV protease.
Authors: Perryman, A.L. / Zhang, Q. / Soutter, H.H. / Rosenfeld, R. / McRee, D.E. / Olson, A.J. / Elder, J.E. / David Stout, C.
History
DepositionOct 27, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 23, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Structure summary / Version format compliance
Revision 1.2Feb 27, 2013Group: Other
Revision 1.3Oct 13, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / 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_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protease
B: Protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,07810
Polymers21,6642
Non-polymers1,4148
Water3,801211
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3540 Å2
ΔGint-24 kcal/mol
Surface area10130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.518, 85.910, 46.440
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-349-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Protease


Mass: 10831.833 Da / Num. of mol.: 2
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: Q903N5, UniProt: P12499*PLUS, HIV-1 retropepsin

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Non-polymers , 6 types, 219 molecules

#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-4DX / (1S,2S)-2-methylcyclohexanol / trans-2-methylcyclohexanol


Mass: 114.185 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H14O
#4: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#6: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 211 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.74 Å3/Da / Density % sol: 55.11 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 5.8
Details: 0.5 M KSCN, 0.1 M MES-HCL, pH 5.8, 10% DMSO, VAPOR DIFFUSION, temperature 277.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.97945 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jul 26, 2008
Details: Monochromator:Side scattering bent cube-root I-beam single crystal; asymmetric cut 4.965 degs; Mirrors: Rh coated flat mirror
RadiationMonochromator: Monochromator:Side scattering bent cube-root I-beam single crystal; asymmetric cut 4.965 degs;
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97945 Å / Relative weight: 1
ReflectionResolution: 1.8→31.53 Å / Num. all: 22686 / Num. obs: 21597 / % possible obs: 95.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Biso Wilson estimate: 23.1 Å2 / Rmerge(I) obs: 0.064 / Rsym value: 0.064 / Net I/σ(I): 5.5
Reflection shellResolution: 1.8→1.85 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.183 / Mean I/σ(I) obs: 3.8 / Num. unique all: 3398 / Rsym value: 0.183 / % possible all: 75.4

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0090refinement
PDB_EXTRACT3.005data extraction
Blu-Icedata collection
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Dimer generated from PDB entry 2AZ8

2az8


Resolution: 1.8→31.53 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.937 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 3.079 / SU ML: 0.097 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.14 / ESU R Free: 0.134 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS; U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.246 1106 5.1 %RANDOM
Rwork0.206 ---
obs0.208 21566 95.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 95.55 Å2 / Biso mean: 27.867 Å2 / Biso min: 15.1 Å2
Baniso -1Baniso -2Baniso -3
1-2.82 Å20 Å20 Å2
2---1.75 Å20 Å2
3----1.06 Å2
Refinement stepCycle: LAST / Resolution: 1.8→31.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1518 0 92 211 1821
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0211829
X-RAY DIFFRACTIONr_angle_refined_deg1.0641.9932801
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3367.5392
X-RAY DIFFRACTIONr_dihedral_angle_2_deg43.32424.81554
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.34615288
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.615158
X-RAY DIFFRACTIONr_chiral_restr0.0820.2257
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0211984
X-RAY DIFFRACTIONr_mcbond_it0.6691.5977
X-RAY DIFFRACTIONr_mcangle_it1.26221588
X-RAY DIFFRACTIONr_scbond_it1.9323656
X-RAY DIFFRACTIONr_scangle_it3.364.5615
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.314 59 -
Rwork0.239 1162 -
all-1221 -
obs-1162 75.4 %

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