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- PDB-4ydg: Crystal structure of compound 10 in complex with HTLV-1 Protease -

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Basic information

Entry
Database: PDB / ID: 4ydg
TitleCrystal structure of compound 10 in complex with HTLV-1 Protease
ComponentsHTLV-1 protease
KeywordsHYDROLASE / HTLV-1 protease
Function / homology
Function and homology information


Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / ribonuclease H / DNA integration / RNA-directed DNA polymerase / viral genome integration into host DNA / establishment of integrated proviral latency / RNA-directed DNA polymerase activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / RNA-DNA hybrid ribonuclease activity / viral nucleocapsid ...Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / ribonuclease H / DNA integration / RNA-directed DNA polymerase / viral genome integration into host DNA / establishment of integrated proviral latency / RNA-directed DNA polymerase activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / RNA-DNA hybrid ribonuclease activity / 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 / symbiont-mediated suppression of host gene expression / structural molecule activity / proteolysis / DNA binding / RNA binding / zinc ion binding
Similarity search - Function
Delta-retroviral matrix protein / Major core protein p19 / gag protein p24 N-terminal domain / Integrase Zinc binding domain / 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. / RNase H ...Delta-retroviral matrix protein / Major core protein p19 / gag protein p24 N-terminal domain / Integrase Zinc binding domain / 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. / 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 / 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. / Ribonuclease H superfamily / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / 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-G3G / Gag-Pro-Pol polyprotein
Similarity search - Component
Biological speciesHuman T-cell leukemia virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.25 Å
AuthorsKuhnert, M. / Blum, A. / Steuber, H. / Diederich, W.E.
CitationJournal: J.Med.Chem. / Year: 2015
Title: Privileged Structures Meet Human T-Cell Leukemia Virus-1 (HTLV-1): C2-Symmetric 3,4-Disubstituted Pyrrolidines as Nonpeptidic HTLV-1 Protease Inhibitors.
Authors: Kuhnert, M. / Blum, A. / Steuber, H. / Diederich, W.E.
History
DepositionFeb 22, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Feb 3, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: 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

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Assembly

Deposited unit
A: HTLV-1 protease
B: HTLV-1 protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,9175
Polymers25,1332
Non-polymers7843
Water0
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4550 Å2
ΔGint-34 kcal/mol
Surface area11030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.610, 77.610, 160.230
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322

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Components

#1: Protein HTLV-1 protease / Pr160Gag-Pro-Pol


Mass: 12566.579 Da / Num. of mol.: 2 / Fragment: residues 450-565 / Mutation: L40I
Source method: isolated from a genetically manipulated source
Details: Parts of the flap region omitted from structural model due to to disorder.
Source: (gene. exp.) Human T-cell leukemia virus 1 (strain Japan ATK-1 subtype A)
Gene: gag-pro-pol / Production host: Escherichia coli (E. coli)
References: UniProt: P03362, Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases, RNA-directed DNA polymerase, DNA-directed DNA polymerase, ribonuclease H
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-G3G / N,N'-(3S,4S)-PYRROLIDINE-3,4-DIYLBIS(4-AMINO-N-BENZYLBENZENESULFONAMIDE)


Mass: 591.744 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C30H33N5O4S2

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.56 Å3/Da / Density % sol: 52 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 1.3 M ammonium sulfate, 20 % glycerol, 0.1 M Tris pH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 23, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 3.25→50 Å / Num. obs: 4746 / % possible obs: 96.3 % / Redundancy: 14.3 % / Rmerge(I) obs: 0.294 / Net I/σ(I): 8.6
Reflection shellResolution: 3.25→3.5 Å / Redundancy: 14.9 % / Rmerge(I) obs: 0.826 / Mean I/σ(I) obs: 3.22 / % possible all: 97.4

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8.1_1168)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3LIX

3lix


Resolution: 3.25→41.9 Å / Cross valid method: FREE R-VALUE / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3166 238 5.02 %
Rwork0.279 --
obs0.2809 4737 96.24 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.25→41.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1693 0 51 0 1744
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031786
X-RAY DIFFRACTIONf_angle_d0.6942454
X-RAY DIFFRACTIONf_dihedral_angle_d18.905666
X-RAY DIFFRACTIONf_chiral_restr0.045309
X-RAY DIFFRACTIONf_plane_restr0.007304
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2542-4.09940.3451150.30382185X-RAY DIFFRACTION97
4.0994-41.81860.29951230.26362314X-RAY DIFFRACTION95
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)
14.42110.5876-1.32.5688-3.08971.555-0.0452-0.2961-0.20590.0919-0.07510.28040.0043-0.16040.12130.30720.00490.00340.2538-0.11790.3755-12.099665.3621180.3835
26.0110.70021.64283.93920.77052.7565-0.1466-0.2184-0.00450.4025-0.1121-0.25850.07310.05320.1270.3030.030.04330.22590.0060.175911.95569.0528180.5482
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and resid 1:116
2X-RAY DIFFRACTION2chain B and resid 1:116

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