2TMK

YEAST THYMIDYLATE KINASE COMPLEXED WITH 3'-AZIDO-3'-DEOXYTHYMIDINE MONOPHOSPHATE (AZT-MP)

PDB DOI: https://doi.org/10.2210/pdb2TMK/pdb

Classification: PHOSPHOTRANSFERASE
Organism(s): Saccharomyces cerevisiae
Expression System: Escherichia coli
Mutation(s): No

Deposited: 1997-06-12 Released: 1998-06-17
Deposition Author(s): Lavie, A., Schlichting, I.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.253
R-Value Work: 0.182
R-Value Observed: 0.182

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 1.5 of the entry. See complete history.

Literature

Structure of thymidylate kinase reveals the cause behind the limiting step in AZT activation.

Lavie, A., Vetter, I.R., Konrad, M., Goody, R.S., Reinstein, J., Schlichting, I.

(1997) Nat Struct Biol 4: 601-604

PubMed: 9253404 Search on PubMed
DOI: https://doi.org/10.1038/nsb0897-601
Primary Citation of Related Structures:
1TMK, 2TMK

Macromolecule Content

Total Structure Weight: 50.33 kDa
Atom Count: 3,518
Modelled Residue Count: 408
Deposited Residue Count: 432
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
THYMIDYLATE KINASE	A, B	216	Saccharomyces cerevisiae	Mutation(s): 0 Gene Names: CDC8 EC: 2.7.4.9
UniProt
Find proteins for P00572 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P00572 Go to UniProtKB: P00572
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P00572
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ATM Query on ATM 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] mmCIF format, chain D [auth A] mmCIF format, chain F [auth B]	D [auth A], F [auth B]	3'-AZIDO-3'-DEOXYTHYMIDINE-5'-MONOPHOSPHATE C₁₀ H₁₄ N₅ O₇ P OIFWQOKDSPDILA-XLPZGREQSA-N		Interactions Focus chain D [auth A] Focus chain F [auth B] Interactions & Density Focus chain D [auth A] Focus chain F [auth B]
SO4 Query on SO4 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] mmCIF format, chain C [auth A] mmCIF format, chain E [auth B]	C [auth A], E [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain C [auth A] Focus chain E [auth B] Interactions & Density Focus chain C [auth A] Focus chain E [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.253
R-Value Work: 0.182
R-Value Observed: 0.182
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 37.42	α = 90
b = 144.2	β = 110.9
c = 49.72	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	model building
X-PLOR	refinement
DENZO	data reduction
SCALEPACK	data scaling
X-PLOR	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 1998-06-17

Deposition Author(s):

Lavie, A.

Schlichting, I.

Revision History (Full details and data files)

Version 1.0: 1998-06-17
Type: Initial release
Version 1.1: 2008-03-25
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2018-04-04
Changes: Data collection, Other
Version 1.4: 2023-08-09
Changes: Database references, Derived calculations, Refinement description
Version 1.5: 2024-05-22
Changes: Data collection

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Help and Resources

2TMK

YEAST THYMIDYLATE KINASE COMPLEXED WITH 3'-AZIDO-3'-DEOXYTHYMIDINE MONOPHOSPHATE (AZT-MP)

Structure of thymidylate kinase reveals the cause behind the limiting step in AZT activation.

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)