[English] 日本語
Yorodumi
- PDB-1xbt: Crystal Structure of Human Thymidine Kinase 1 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1xbt
TitleCrystal Structure of Human Thymidine Kinase 1
ComponentsThymidine kinase, cytosolic
KeywordsTRANSFERASE / DEOXYRIBONUCLEOSIDE KINASE / ZINC-BINDING DOMAIN / FEEDBACK INHIBITOR
Function / homology
Function and homology information


DNA synthesis involved in mitotic DNA replication / thymidine biosynthetic process / thymidine metabolic process / thymidine kinase / thymidine kinase activity / Pyrimidine salvage / nucleobase-containing compound metabolic process / G1/S-Specific Transcription / protein homotetramerization / phosphorylation ...DNA synthesis involved in mitotic DNA replication / thymidine biosynthetic process / thymidine metabolic process / thymidine kinase / thymidine kinase activity / Pyrimidine salvage / nucleobase-containing compound metabolic process / G1/S-Specific Transcription / protein homotetramerization / phosphorylation / zinc ion binding / ATP binding / identical protein binding / nucleus / cytosol
Similarity search - Function
Thymidine kinase / Thymidine kinase, conserved site / Thymidine kinase / Thymidine kinase cellular-type signature. / Wheat Germ Agglutinin (Isolectin 2); domain 1 - #20 / Wheat Germ Agglutinin (Isolectin 2); domain 1 / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 2-Layer Sandwich ...Thymidine kinase / Thymidine kinase, conserved site / Thymidine kinase / Thymidine kinase cellular-type signature. / Wheat Germ Agglutinin (Isolectin 2); domain 1 - #20 / Wheat Germ Agglutinin (Isolectin 2); domain 1 / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
THYMIDINE-5'-TRIPHOSPHATE / Thymidine kinase, cytosolic
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 2.4 Å
AuthorsWelin, M. / Kosinska, U. / Mikkelsen, N.E. / Carnrot, C. / Zhu, C. / Wang, L. / Eriksson, S. / Munch-Petersen, B. / Eklund, H.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2004
Title: Structures of thymidine kinase 1 of human and mycoplasmic origin
Authors: Welin, M. / Kosinska, U. / Mikkelsen, N.E. / Carnrot, C. / Zhu, C. / Wang, L. / Eriksson, S. / Munch-Petersen, B. / Eklund, H.
History
DepositionAug 31, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 14, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Thymidine kinase, cytosolic
B: Thymidine kinase, cytosolic
C: Thymidine kinase, cytosolic
D: Thymidine kinase, cytosolic
E: Thymidine kinase, cytosolic
F: Thymidine kinase, cytosolic
G: Thymidine kinase, cytosolic
H: Thymidine kinase, cytosolic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)175,19132
Polymers170,6168
Non-polymers4,57524
Water3,837213
1
A: Thymidine kinase, cytosolic
B: Thymidine kinase, cytosolic
C: Thymidine kinase, cytosolic
D: Thymidine kinase, cytosolic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,59616
Polymers85,3084
Non-polymers2,28812
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12360 Å2
ΔGint-93 kcal/mol
Surface area25830 Å2
MethodPISA
2
E: Thymidine kinase, cytosolic
F: Thymidine kinase, cytosolic
G: Thymidine kinase, cytosolic
H: Thymidine kinase, cytosolic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,59616
Polymers85,3084
Non-polymers2,28812
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12430 Å2
ΔGint-98 kcal/mol
Surface area26040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)157.672, 123.177, 116.000
Angle α, β, γ (deg.)90.00, 130.20, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F
71G
81H
91A
101B
111C
121D
131E
141F
151G
161H

NCS domain segments:

Ens-ID: 1 / Refine code: 2

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ARGARGASPASPAA18 - 5818 - 58
21ARGARGASPASPBB18 - 5818 - 58
31ARGARGASPASPCC18 - 5818 - 58
41ARGARGASPASPDD18 - 5818 - 58
51ARGARGASPASPEE18 - 5818 - 58
61ARGARGASPASPFF18 - 5818 - 58
71ARGARGASPASPGG18 - 5818 - 58
81ARGARGASPASPHH18 - 5818 - 58
92ALAALALYSLYSAA75 - 19175 - 191
102ALAALALYSLYSBB75 - 19175 - 191
112ALAALALYSLYSCC75 - 19175 - 191
122ALAALALYSLYSDD75 - 19175 - 191
132ALAALALYSLYSEE75 - 19175 - 191
142ALAALALYSLYSFF75 - 19275 - 192
152ALAALALYSLYSGG75 - 19175 - 191
162ALAALALYSLYSHH75 - 19175 - 191

-
Components

#1: Protein
Thymidine kinase, cytosolic / / DEOXYRIBONUCLEOSIDE KINASE


Mass: 21327.000 Da / Num. of mol.: 8 / Fragment: Truncation mutant(residues 1-193)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TK1 / Plasmid: pGEX-2T / Production host: Escherichia coli (E. coli) / References: UniProt: P04183, thymidine kinase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-TTP / THYMIDINE-5'-TRIPHOSPHATE / Thymidine triphosphate


Mass: 482.168 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C10H17N2O14P3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 213 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 3 Å3/Da / Density % sol: 58.7 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: sodium citrate, 2-propanol, PEG 4000, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 288.0K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 2, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.25→87.7 Å / Num. all: 77566 / Num. obs: 77566 / % possible obs: 28.4 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.5 % / Rsym value: 0.101 / Net I/σ(I): 4.9
Reflection shellResolution: 2.25→2.37 Å / Redundancy: 3.5 % / Mean I/σ(I) obs: 1.5 / Num. unique all: 11361 / Rsym value: 0.434 / % possible all: 98.6

-
Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
autoSHARPphasing
RefinementMethod to determine structure: SIRAS / Resolution: 2.4→42.07 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.914 / SU B: 6.798 / SU ML: 0.16 / Cross valid method: THROUGHOUT / ESU R: 0.354 / ESU R Free: 0.233 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.23204 3317 5.1 %RANDOM
Rwork0.20133 ---
obs0.20288 62088 98.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 34.695 Å2
Baniso -1Baniso -2Baniso -3
1-2.86 Å20 Å21.78 Å2
2---0.5 Å20 Å2
3----0.07 Å2
Refinement stepCycle: LAST / Resolution: 2.4→42.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9990 0 248 213 10451
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.02210377
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2591.99914005
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.61951273
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0880.21593
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.027504
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1840.24395
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1430.2482
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.2350.28
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1760.255
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.110.210
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it0.5191.56373
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.024210216
X-RAY DIFFRACTIONr_scbond_it1.46134004
X-RAY DIFFRACTIONr_scangle_it2.5414.53789
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A632tight positional0.030.05
2B632tight positional0.030.05
3C632tight positional0.030.05
4D632tight positional0.030.05
5E632tight positional0.030.05
6F632tight positional0.030.05
7G632tight positional0.030.05
8H632tight positional0.030.05
1A589medium positional0.440.5
2B589medium positional0.410.5
3C589medium positional0.480.5
4D589medium positional0.390.5
5E589medium positional0.440.5
6F589medium positional0.410.5
7G589medium positional0.380.5
8H589medium positional0.430.5
1A632tight thermal0.050.5
2B632tight thermal0.060.5
3C632tight thermal0.080.5
4D632tight thermal0.060.5
5E632tight thermal0.050.5
6F632tight thermal0.060.5
7G632tight thermal0.080.5
8H632tight thermal0.060.5
1A589medium thermal0.412
2B589medium thermal0.42
3C589medium thermal0.592
4D589medium thermal0.42
5E589medium thermal0.462
6F589medium thermal0.432
7G589medium thermal0.52
8H589medium thermal0.422
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.28 246
Rwork0.241 4560

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more