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- PDB-6w6s: WT HTLV-1 Protease in Complex with Phosphonated UMass6 (PU6) -

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Basic information

Entry
Database: PDB / ID: 6w6s
TitleWT HTLV-1 Protease in Complex with Phosphonated UMass6 (PU6)
ComponentsHTLV-1 Protease
KeywordsHYDROLASE/HYDROLASE INHIBITOR / HTLV / PROTEASE / PROTEASE INHIBITOR / COMPLEX / HYDROLASE INHIBITOR COMPLEX / HYDROLASE / HYDROLASE-HYDROLASE INHIBITOR COMPLEX
Function / homology
Function and homology information


aspartic-type endopeptidase activity / proteolysis
Similarity search - Function
Retropepsins / Retroviral aspartyl protease / Aspartyl protease, retroviral-type family profile. / Peptidase A2A, retrovirus, catalytic / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Aspartic peptidase domain superfamily
Similarity search - Domain/homology
Chem-TK7 / Pro protein
Similarity search - Component
Biological speciesHuman T-cell leukemia virus type I
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.29 Å
AuthorsLockbaum, G.J. / Henes, M. / Kosovrasti, K. / Nalivaika, E.A. / Ali, A. / KurtYilmaz, N. / Schiffer, C.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P01-GM109767 United States
CitationJournal: To Be Published
Title: To Be Determined
Authors: Lockbaum, G.J. / Henes, M. / Kosovrasti, K. / Nalivaika, E.A. / Ali, A. / KurtYilmaz, N. / Schiffer, C.A.
History
DepositionMar 17, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 17, 2021Provider: repository / Type: Initial release
Revision 2.0Oct 18, 2023Group: Data collection / Database references ...Data collection / Database references / Non-polymer description / Refinement description
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _chem_comp.formula / _database_2.pdbx_DOI ..._chem_comp.formula / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)25,8753
Polymers25,1332
Non-polymers7421
Water43224
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4370 Å2
ΔGint-24 kcal/mol
Surface area10230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.566, 76.566, 157.285
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number182
Space group name H-MP6322
Components on special symmetry positions
IDModelComponents
11A-310-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 1 through 9 or resid 11...
21(chain B and (resid 1 through 9 or resid 11...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PROPROARGARG(chain A and (resid 1 through 9 or resid 11...AB1 - 91 - 9
12PROPROPROPRO(chain A and (resid 1 through 9 or resid 11...AB11 - 2411 - 24
13LYSLYSLYSLYS(chain A and (resid 1 through 9 or resid 11...AB2525
14PROPROPROPRO(chain A and (resid 1 through 9 or resid 11...AB1 - 1161 - 116
15PROPROPROPRO(chain A and (resid 1 through 9 or resid 11...AB1 - 1161 - 116
16PROPROPROPRO(chain A and (resid 1 through 9 or resid 11...AB1 - 1161 - 116
17PROPROPROPRO(chain A and (resid 1 through 9 or resid 11...AB1 - 1161 - 116
21PROPROARGARG(chain B and (resid 1 through 9 or resid 11...BA1 - 91 - 9
22PROPROILEILE(chain B and (resid 1 through 9 or resid 11...BA11 - 1311 - 13
23LYSLYSALAALA(chain B and (resid 1 through 9 or resid 11...BA14 - 1514 - 15
24PROPROPROPRO(chain B and (resid 1 through 9 or resid 11...BA1 - 1161 - 116
25PROPROPROPRO(chain B and (resid 1 through 9 or resid 11...BA1 - 1161 - 116
26PROPROPROPRO(chain B and (resid 1 through 9 or resid 11...BA1 - 1161 - 116
27PROPROPROPRO(chain B and (resid 1 through 9 or resid 11...BA1 - 1161 - 116

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Components

#1: Protein HTLV-1 Protease


Mass: 12566.579 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human T-cell leukemia virus type I / Gene: pro / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1Y1C9N2
#2: Chemical ChemComp-TK7 / diethyl [(4-{(2S,3R)-4-{[(4-aminophenyl)sulfonyl](2-ethylbutyl)amino}-2-[({[(3R,3aS,6aR)-hexahydrofuro[2,3-b]furan-3-yl]oxy}carbonyl)amino]-3-hydroxybutyl}phenoxy)methyl]phosphonate


Mass: 741.829 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C34H52N3O11PS / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 24 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.65 Å3/Da / Density % sol: 53.54 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.2
Details: 39-41% (v/v) PEG 300, 0.1M Phosphate/Citrate Buffer pH 4.2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.07812 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 20, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07812 Å / Relative weight: 1
ReflectionResolution: 2.29→41.126 Å / Num. obs: 114508 / % possible obs: 99.85 % / Redundancy: 8.8 % / Biso Wilson estimate: 61.3 Å2 / CC1/2: 0.993 / CC star: 0.998 / Rpim(I) all: 0.08747 / Net I/σ(I): 5.9
Reflection shellResolution: 2.29→2.372 Å / Mean I/σ(I) obs: 0.93 / Num. unique obs: 11155 / CC1/2: 0.145 / CC star: 0.503 / Rpim(I) all: 1.36

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
Aimlessdata scaling
PHASERphasing
Coot0.8.8model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3wsj

3wsj


Resolution: 2.29→41.126 Å / SU ML: 0.42 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 39.27
RfactorNum. reflection% reflection
Rfree0.3056 647 5 %
Rwork0.2656 --
obs0.2677 12949 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 164.69 Å2 / Biso mean: 76.0541 Å2 / Biso min: 34.81 Å2
Refinement stepCycle: final / Resolution: 2.29→41.126 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1676 0 102 24 1802
Biso mean--93.34 70.02 -
Num. residues----232
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071777
X-RAY DIFFRACTIONf_angle_d0.8822457
X-RAY DIFFRACTIONf_dihedral_angle_d9.3211239
X-RAY DIFFRACTIONf_chiral_restr0.058318
X-RAY DIFFRACTIONf_plane_restr0.005306
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A684X-RAY DIFFRACTION5.869TORSIONAL
12B684X-RAY DIFFRACTION5.869TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
2.29-2.46680.38581260.36182393
2.4668-2.7150.37941250.34752389
2.715-3.10780.44141280.37952409
3.1078-3.9150.28561290.26192468
3.915-41.1260.27411390.22852643

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