Macromolecule Content

Total Structure Weight: 52.91 kDa
Atom Count: 4170
Modelled Residue Count: 420
Deposited Residue Count: 426
Unique protein chains: 1

2PLR

Crystal structure of dTMP kinase (st1543) from Sulfolobus Tokodaii Strain7

DOI: 10.2210/pdb2PLR/pdb

Classification: TRANSFERASE
Organism(s): Sulfurisphaera tokodaii str. 7
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2007-04-20 Released: 2008-04-22
Deposition Author(s): Kanaujia, S.P., Jeyakanthan, J., Rafi, Z.A., Sekar, K., Nakagawa, N., Ebihara, A., Kuramitsu, S., Shinkai, A., Shiro, Y., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free: 0.209
R-Value Work: 0.185
R-Value Observed: 0.185

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Crystal structure of dTMP kinase (st1543) from Sulfolobus Tokodaii Strain7

Kanaujia, S.P., Jeyakanthan, J., Rafi, Z.A., Sekar, K., Nakagawa, N., Ebihara, A., Kuramitsu, S., Shinkai, A., Shiro, Y., Yokoyama, S.

To be published.

Macromolecules

Find similar proteins by:

(by identity cutoff) | Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable thymidylate kinase	A, B	213	Sulfurisphaera tokodaii str. 7	Mutation(s): 0 Gene Names: tmk, STK_15430 EC: 2.7.4.9
Find proteins for Q970Q8 (Sulfurisphaera tokodaii (strain DSM 16993 / JCM 10545 / NBRC 100140 / 7)) Explore Q970Q8 Go to UniProtKB: Q970Q8
Protein Feature View Expand
Reference Sequence

Small Molecules

Ligands 9 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EPE Query on EPE Download Ideal Coordinates CCD File SDF format, chain N [A] MOL2 format, chain N [A]	A	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C₈ H₁₈ N₂ O₄ S JKMHFZQWWAIEOD-UHFFFAOYSA-N		Ligand Interaction
1PE Query on 1PE Download Ideal Coordinates CCD File SDF format, chain F [A] SDF format, chain V [B] SDF format, chain W [B] MOL2 format, chain F [A] MOL2 format, chain V [B] MOL2 format, chain W [B]	A, B	PENTAETHYLENE GLYCOL C₁₀ H₂₂ O₆ JLFNLZLINWHATN-UHFFFAOYSA-N		Ligand Interaction
PG4 Query on PG4 Download Ideal Coordinates CCD File SDF format, chain AA [B] MOL2 format, chain AA [B]	B	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Ligand Interaction
DTT Query on DTT Download Ideal Coordinates CCD File SDF format, chain M [A] MOL2 format, chain M [A]	A	2,3-DIHYDROXY-1,4-DITHIOBUTANE C₄ H₁₀ O₂ S₂ VHJLVAABSRFDPM-IMJSIDKUSA-N		Ligand Interaction
PGE Query on PGE Download Ideal Coordinates CCD File SDF format, chain G [A] SDF format, chain H [A] SDF format, chain I [A] MOL2 format, chain G [A] MOL2 format, chain H [A] MOL2 format, chain I [A]	A	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Ligand Interaction
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain BA [B] SDF format, chain CA [B] SDF format, chain DA [B] SDF format, chain EA [B] SDF format, chain O [A] SDF format, chain P [A] SDF format, chain Q [A] SDF format, chain R [A] SDF format, chain S [A] SDF format, chain T [A] SDF format, chain U [A] MOL2 format, chain BA [B] MOL2 format, chain CA [B] MOL2 format, chain DA [B] MOL2 format, chain EA [B] MOL2 format, chain O [A] MOL2 format, chain P [A] MOL2 format, chain Q [A] MOL2 format, chain R [A] MOL2 format, chain S [A] MOL2 format, chain T [A] MOL2 format, chain U [A]	A, B	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Ligand Interaction
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain E [A] MOL2 format, chain E [A]	A	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Ligand Interaction
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain J [A] SDF format, chain K [A] SDF format, chain L [A] SDF format, chain X [B] SDF format, chain Y [B] SDF format, chain Z [B] MOL2 format, chain J [A] MOL2 format, chain K [A] MOL2 format, chain L [A] MOL2 format, chain X [B] MOL2 format, chain Y [B] MOL2 format, chain Z [B]	A, B	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Ligand Interaction
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain C [A] SDF format, chain D [A] MOL2 format, chain C [A] MOL2 format, chain D [A]	A	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Ligand Interaction

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A,B	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free: 0.209
R-Value Work: 0.185
R-Value Observed: 0.185
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.523	α = 90
b = 62.873	β = 90
c = 137.332	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
HKL-2000	data collection
HKL-2000	data reduction
SCALEPACK	data scaling
MOLREP	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Deposited Date: 2007-04-20
Released Date: 2008-04-22

Deposition Author(s):

Jeyakanthan, J.

RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History (Full details and data files)

Version 1.0: 2008-04-22
Type: Initial release
Version 1.1: 2011-07-13
Changes: Source and taxonomy, Version format compliance

RCSB PDB is funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.