1XX6

X-ray structure of Clostridium acetobutylicum thymidine kinase with ADP. Northeast Structural Genomics Target CAR26.

PDB DOI: https://doi.org/10.2210/pdb1XX6/pdb

Classification: TRANSFERASE
Organism(s): Clostridium acetobutylicum ATCC 824
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2004-11-04 Released: 2004-12-21
Deposition Author(s): Kuzin, A.P., Abashidze, M., Forouhar, F., Vorobiev, S.M., Acton, T.B., Ma, L.-C., Xiao, R., Montelione, G.T., Tong, L., Hunt, J.F., Northeast Structural Genomics Consortium (NESG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.266
R-Value Work: 0.241
R-Value Observed: 0.241

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

X-ray structure of Clostridium acetobutylicum thymidine kinase with ADP. Northeast Structural Genomics Target CAR26.

Kuzin, A.P., Abashidze, M., Forouhar, F., Vorobiev, S.M., Acton, T.B., Ma, L.-C., Xiao, R., Montelione, G.T., Tong, L., Hunt, J.F.

To be published.

Macromolecule Content

Total Structure Weight: 45.15 kDa
Atom Count: 2,988
Modelled Residue Count: 344
Deposited Residue Count: 382
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thymidine kinase	A, B	191	Clostridium acetobutylicum ATCC 824	Mutation(s): 5 EC: 2.7.1.21
UniProt
Find proteins for Q97F65 (Clostridium acetobutylicum (strain ATCC 824 / DSM 792 / JCM 1419 / LMG 5710 / VKM B-1787)) Explore Q97F65 Go to UniProtKB: Q97F65
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q97F65
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ADP Query on ADP Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain F [auth B] MOL2 format, chain D [auth A] MOL2 format, chain F [auth B]	D [auth A], F [auth B]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain D [auth A] Focus chain F [auth B] Interactions & Density Focus chain D [auth A] Focus chain F [auth B]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain E [auth B] MOL2 format, chain C [auth A] MOL2 format, chain E [auth B]	C [auth A], E [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain E [auth B] Interactions & Density Focus chain C [auth A] Focus chain E [auth B]

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: 2.00 Å
R-Value Free: 0.266
R-Value Work: 0.241
R-Value Observed: 0.241
Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.793	α = 90
b = 67.166	β = 90
c = 103.638	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
SOLVE	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2004-12-21

Deposition Author(s):

Northeast Structural Genomics Consortium (NESG)

Revision History (Full details and data files)

Version 1.0: 2004-12-21
Type: Initial release
Version 1.1: 2008-04-30
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Source and taxonomy, Version format compliance
Version 1.3: 2024-03-06
Changes: Data collection, Database references, Derived calculations

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1XX6

X-ray structure of Clostridium acetobutylicum thymidine kinase with ADP. Northeast Structural Genomics Target CAR26.

X-ray structure of Clostridium acetobutylicum thymidine kinase with ADP. Northeast Structural Genomics Target CAR26.

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Expand

Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)