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- PDB-1e2m: HPT + HMTT -

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Basic information

Entry
Database: PDB / ID: 1e2m
TitleHPT + HMTT
ComponentsTHYMIDINE KINASE
KeywordsTRANSFERASE
Function / homology
Function and homology information


TMP biosynthetic process / thymidine kinase / thymidine kinase activity / DNA biosynthetic process / phosphorylation / ATP binding
Similarity search - Function
Herpesvirus thymidine kinase / Thymidine kinase from herpesvirus / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
6-HYDROXYPROPYLTHYMINE / Thymidine kinase / Thymidine kinase
Similarity search - Component
Biological speciesHERPES SIMPLEX VIRUS
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsVogt, J. / Scapozza, L. / Schulz, G.E.
Citation
Journal: Protein Sci. / Year: 2001
Title: The Effect of Substrate Binding on the Conformation and Structural Stability of Herpes Simplex Virus Type 1 Thymidine Kinase
Authors: Wurth, C. / Kessler, U. / Vogt, J. / Schulz, G.E. / Folkers, G. / Scapozza, L.
#1: Journal: FEBS Lett. / Year: 1995
Title: The Three-Dimensional Structure of Thymidine Kinase from Herpes Simplex Virus Type 1
Authors: Wild, K. / Bohner, T. / Aubry, A. / Folkers, G. / Schulz, G.E.
#2: Journal: Nat.Struct.Biol. / Year: 1995
Title: Crystal Structures of the Thymidine Kinase from Herpes Simplex Virus Type-1 in Complex with Deoxythymidine and Ganciclovir
Authors: Brown, D.G. / Visse, R. / Sandhu, G. / Davies, A. / Rizkallah, P.J. / Melitz, C. / Summers, W.C. / Sanderson, M.R.
History
DepositionMay 23, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 31, 2001Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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: THYMIDINE KINASE
B: THYMIDINE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,1196
Polymers71,5582
Non-polymers5614
Water4,125229
1
A: THYMIDINE KINASE
B: THYMIDINE KINASE
hetero molecules

A: THYMIDINE KINASE
B: THYMIDINE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)144,23712
Polymers143,1164
Non-polymers1,1218
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_565x,-y+1,-z1
Buried area11860 Å2
ΔGint-157.99 kcal/mol
Surface area43990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.700, 117.200, 108.500
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.92428, -0.32871, -0.19407), (-0.32663, 0.41794, 0.84773), (-0.19755, 0.84692, -0.49366)
Vector: 74.93742, 22.90658, -9.49576)
DetailsTHE STRONG CRYSTAL PACKING GENERATED USING X , 1-Y, -Z GIVESCHAIN A TO CHAIN A (SYMMETRY RELATED) CONTACTS.

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Components

#1: Protein THYMIDINE KINASE


Mass: 35779.086 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HERPES SIMPLEX VIRUS (TYPE 1 / STRAIN 17)
Strain: 17 / Production host: ESCHERICHIA COLI (E. coli)
References: UniProt: P03176, UniProt: P0DTH5*PLUS, thymidine kinase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-HPT / 6-HYDROXYPROPYLTHYMINE


Mass: 184.192 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H12N2O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 229 / 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: 2.53 Å3/Da / Density % sol: 51.3 %
Crystal growpH: 7.5 / Details: LITHIUM SULFATE, HEPES, DTT, pH 7.50
Crystal grow
*PLUS
Temperature: 23 ℃ / pH: 8 / Method: vapor diffusion, hanging drop / Details: Prota, A., (2000) Biochemistry, 39, 9597.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
125 mg/mlprotein1drop
21 mMMCT1drop
30.9-1.2 M1reservoirLiSO4
41 mMdithiothreitol1reservoir
50.1 MHEPES1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU2HC / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 15, 1999
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→20 Å / Num. obs: 36554 / % possible obs: 99 % / Redundancy: 3.8 % / Biso Wilson estimate: 27 Å2 / Rmerge(I) obs: 0.106 / Rsym value: 0.106 / Net I/σ(I): 10.7
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 2.7 / Rsym value: 0.49 / % possible all: 97
Reflection shell
*PLUS
% possible obs: 97 %

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Processing

Software
NameClassification
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTR 1VTK

1vtk


Resolution: 2.2→20 Å / SU B: 3.5 / SU ML: 0.09 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.27 / ESU R Free: 0.22
RfactorNum. reflection% reflectionSelection details
Rfree0.262 1728 5 %RANDOM
Rwork0.217 ---
obs-36554 99 %-
Displacement parametersBiso mean: 28 Å2
Refinement stepCycle: LAST / Resolution: 2.2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4700 0 36 229 4965
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.007
X-RAY DIFFRACTIONp_angle_d0.018
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor

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