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233,605 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Enzyme Classification Number = 2.7.4.1

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Search Summary

This query matches 19 Structures.

Refinements

Structure Determination Methodology

experimental (19)

Scientific Name of Source Organism

	Saccharomyces cerevisiae (7)
	Francisella tularensis subsp. tularensis SCHU S4 (3)
	Saccharomyces cerevisiae S288C (3)
	Escherichia coli (2)
	Homo sapiens (2)
	Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539 (1)
	Francisella tularensis (1)
	Porphyromonas gingivalis (1)
	Sinorhizobium meliloti 1021 (1)

Taxonomy

	Eukaryota (10)
	Bacteria (9)

Experimental Method

	X-RAY DIFFRACTION (17)
	ELECTRON MICROSCOPY (2)

Polymer Entity Type

Protein (19)

Refinement Resolution (Å)

	1.5 - 2.0 (4)
	2.0 - 2.5 (6)
	2.5 - 3.0 (4)
	3.0 - 3.5 (5)

Release Date

	2005 - 2009 (7)
	2015 - 2019 (9)
	2020 - 2024 (3)

Enzyme Classification Name

Transferases (19)

Membrane Protein Annotation

	OPM (2)
	PDBTM (2)
	MemProtMD (1)
	mpstruc (1)

Symmetry Type

	Asymmetric (11)
	Cyclic (7)
	Dihedral (5)

SCOP Classification

	Alpha and beta proteins (a+b) (3)
	All alpha proteins (3)

AllSelected

1 to 19 of 19 Structures

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1XDO \| pdb_00001xdo	Download File View File

Crystal Structure of Escherichia coli Polyphosphate Kinase

Zhu, Y., Huang, W., Lee, S.S., Xu, W.

(2005) EMBO Rep 6: 681-687

Released	2005-06-21
Method	X-RAY DIFFRACTION 3 Å
Organisms	Escherichia coli
Macromolecule	Polyphosphate kinase (protein)

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1XDP \| pdb_00001xdp	Download File View File

Crystal Structure of the E.coli Polyphosphate Kinase in complex with AMPPNP

Zhu, Y., Huang, W., Lee, S.S., Xu, W.

(2005) EMBO Rep 6: 681-687

Released	2005-06-21
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Escherichia coli
Macromolecule	Polyphosphate kinase (protein)
Unique Ligands	ATP, MG

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2O8R \| pdb_00002o8r	Download File View File

Crystal Structure of Polyphosphate Kinase from Porphyromonas Gingivalis

Patskovsky, Y., Toro, R., Sauder, J.M., Dickey, M., Adams, J.M., Ozyurt, S., Wasserman, S.R., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

To be published

Released	2006-12-19
Method	X-RAY DIFFRACTION 2.7 Å
Organisms	Porphyromonas gingivalis
Macromolecule	Polyphosphate kinase (protein)
Unique Ligands	SO4

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3G3Q \| pdb_00003g3q	Download File View File

Crystal structure of a eukaryotic polyphosphate polymerase in complex with a phosphate polymer

Hothorn, M., Scheffzek, K.

(2009) Science 324: 513-516

Released	2009-05-05
Method	X-RAY DIFFRACTION 2.64 Å
Organisms	Saccharomyces cerevisiae
Macromolecule	Vacuolar transporter chaperone 4 (protein)
Unique Ligands	PO4, SO4

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3G3R \| pdb_00003g3r	Download File View File

Crystal structure of a eukaryotic polyphosphate polymerase in complex with AppNHp-Mn2+

Hothorn, M.

(2009) Science 324: 513-516

Released	2009-05-05
Method	X-RAY DIFFRACTION 2 Å
Organisms	Saccharomyces cerevisiae
Macromolecule	Vacuolar transporter chaperone 4 (protein)
Unique Ligands	ANP, MN, NA, SO4

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3G3T \| pdb_00003g3t	Download File View File

Crystal structure of a eukaryotic polyphosphate polymerase in complex with orthophosphate

Lenherr, E.D., Hothorn, M., Scheffzek, K.

(2009) Science 324: 513-516

Released	2009-05-05
Method	X-RAY DIFFRACTION 1.85 Å
Organisms	Saccharomyces cerevisiae
Macromolecule	Vacuolar transporter chaperone 4 (protein)
Unique Ligands	EDO, PO4

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3G3U \| pdb_00003g3u	Download File View File

Crystal structure of a eukaryotic polyphosphate polymerase in complex with pyrophosphate

Hothorn, M.

(2009) Science 324: 513-516

Released	2009-05-05
Method	X-RAY DIFFRACTION 2.07 Å
Organisms	Saccharomyces cerevisiae
Macromolecule	Vacuolar transporter chaperone 4 (protein)
Unique Ligands	EDO, POP, SO4

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4YEG \| pdb_00004yeg	Download File View File

Characterisation of Polyphosphate Kinase 2 from the Intracellular Pathogen Francisella tularensis

Parnell, A.E., Roach, P.L.

(2016) Biosci Rep 36: e00294-e00294

Released	2015-12-02
Method	X-RAY DIFFRACTION 2.23 Å
Organisms	Francisella tularensis
Macromolecule	Polyphosphate kinase 2 (protein)

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5IIG \| pdb_00005iig	Download File View File

Structure of the SPX-TTM domain fragment of the yeast inorganic polyphophate polymerase Vtc4 (form A).

Wild, R., Hothorn, M.

(2016) Science 352: 986-990

Released	2016-04-27
Method	X-RAY DIFFRACTION 2.99 Å
Organisms	Saccharomyces cerevisiae
Macromolecule	Vacuolar transporter chaperone 4 (protein)
Unique Ligands	SO4

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5IIQ \| pdb_00005iiq	Download File View File

Structure of the SPX-TTM domain fragment of the yeast inorganic polyphophate polymerase Vtc4 (form B).

Wild, R., Hothorn, M.

(2016) Science 352: 986-990

Released	2016-04-27
Method	X-RAY DIFFRACTION 3.03 Å
Organisms	Saccharomyces cerevisiae
Macromolecule	Vacuolar transporter chaperone 4 (protein)
Unique Ligands	POP, SO4

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5IIT \| pdb_00005iit	Download File View File

Structure of SPX domain of the yeast inorganic polyphophate polymerase Vtc4 crystallized by carrier-driven crystallization in fusion with the macro domain of human histone macroH2A1.1

Wild, R., Hothorn, M.

(2016) Science 352: 986-990

Released	2016-04-27
Method	X-RAY DIFFRACTION 2.134 Å
Organisms	Homo sapiens Saccharomyces cerevisiae S288C
Macromolecule	Vacuolar transporter chaperone 4,Core histone macro-H2A.1 (protein)
Unique Ligands	EDO, MES, MG, SO4

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5LL0 \| pdb_00005ll0	Download File View File

Structure of Polyphosphate Kinase 2 from Francisella tularensis SCHU S4 with polyphosphate

Roach, P.L., Parnell, A.E.

(2018) Proc Natl Acad Sci U S A 115: 3350-3355

Released	2017-10-11
Method	X-RAY DIFFRACTION 1.96 Å
Organisms	Francisella tularensis subsp. tularensis SCHU S4
Macromolecule	Polyphosphate kinase 2 (protein)
Unique Ligands	9PI

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5LLB \| pdb_00005llb	Download File View File

Structure of Polyphosphate Kinase 2 from Francisella tularensis with AMPPCH2PPP and polyphosphate

Roach, P.L., Parnell, A.E.

(2018) Proc Natl Acad Sci U S A 115: 3350-3355

Released	2017-10-11
Method	X-RAY DIFFRACTION 1.92 Å
Organisms	Francisella tularensis subsp. tularensis SCHU S4
Macromolecule	Polyphosphate kinase 2 (protein)
Unique Ligands	6YW, 6YZ, CL, MG

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5LLF \| pdb_00005llf	Download File View File

Structure of Polyphosphate Kinase 2 mutant D117N from Francisella tularensis with polyphosphate

Roach, P.L., Parnell, A.E.

(2018) Proc Natl Acad Sci U S A 115: 3350-3355

Released	2017-10-11
Method	X-RAY DIFFRACTION 2.31 Å
Organisms	Francisella tularensis subsp. tularensis SCHU S4
Macromolecule	Polyphosphate kinase 2 (protein)
Unique Ligands	6YW, 6YX, 6YY, CL, PO4

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5LNC \| pdb_00005lnc	Download File View File

Structure of SPX domain of the yeast inorganic polyphophate polymerase Vtc4 crystallized by carrier-driven crystallization in fusion with the macro domain of human histone macroH2A1.1

Wild, R., Hothorn, M.

(2017) Protein Sci 26: 365-374

Released	2016-11-09
Method	X-RAY DIFFRACTION 3.29 Å
Organisms	Homo sapiens Saccharomyces cerevisiae S288C
Macromolecule	Vacuolar transporter chaperone 4,Core histone macro-H2A.1 (protein)

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6DZG \| pdb_00006dzg	Download File View File

Crystal structure of polyphosphate kinase 2 class I (SMc02148) in complex with ADP

Nocek, B., Joachimiak, A., Ruszkowski, M., Midwest Center for Structural Genomics (MCSG)

To be published

Released	2019-07-10
Method	X-RAY DIFFRACTION 1.87 Å
Organisms	Sinorhizobium meliloti 1021
Macromolecule	Polyphosphate:ADP phosphotransferase 1 (protein)
Unique Ligands	ADP, AMP, MLT

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7BMM \| pdb_00007bmm	Download File View File

Crystal structure of Polyphosphate Kinase 2 from Deinococcus radiodurans in apo form

Silva, S.T.N., Romao, C.

To be published

Released	2021-04-07
Method	X-RAY DIFFRACTION 2.06 Å
Organisms	Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539
Macromolecule	PPK2 domain-containing protein (protein)
Unique Ligands	GOL, PO4

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7YTJ \| pdb_00007ytj	Download File View File

Cryo-EM structure of VTC complex

Guan, Z.Y., Chen, J., Liu, R.W., Chen, Y.K., Xing, Q., Du, Z.M., Liu, Z.

(2023) Nat Commun 14: 718-718

Released	2023-02-22
Method	ELECTRON MICROSCOPY 3 Å
Organisms	Saccharomyces cerevisiae
Macromolecule	Vacuolar transporter chaperone 1 (protein) Vacuolar transporter chaperone 3 (protein) Vacuolar transporter chaperone 4 (protein)
Unique Ligands	IHP, PC1, PO4

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8I6V \| pdb_00008i6v	Download File View File

Cryo-EM structure of the polyphosphate polymerase VTC complex(Vtc4/Vtc3/Vtc1)

Mayer, A., Wu, S., Ye, S.

(2023) EMBO J 42: e113320-e113320

Released	2023-03-01
Method	ELECTRON MICROSCOPY 3.06 Å
Organisms	Saccharomyces cerevisiae S288C
Macromolecule	Vacuolar transporter chaperone 3 complex subunit 3 (protein) Vacuolar transporter chaperone complex subunit 1 (protein) Vacuolar transporter chaperone complex subunit 4 (protein)
Unique Ligands	3PO, MN, PO4, POV

1 to 19 of 19 Structures

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), 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 R01GM157729.

1XDO | pdb_00001xdo

Crystal Structure of Escherichia coli Polyphosphate Kinase

1XDP | pdb_00001xdp

Crystal Structure of the E.coli Polyphosphate Kinase in complex with AMPPNP

2O8R | pdb_00002o8r

Crystal Structure of Polyphosphate Kinase from Porphyromonas Gingivalis

3G3Q | pdb_00003g3q

Crystal structure of a eukaryotic polyphosphate polymerase in complex with a phosphate polymer

3G3R | pdb_00003g3r

Crystal structure of a eukaryotic polyphosphate polymerase in complex with AppNHp-Mn2+

3G3T | pdb_00003g3t

Crystal structure of a eukaryotic polyphosphate polymerase in complex with orthophosphate

3G3U | pdb_00003g3u

Crystal structure of a eukaryotic polyphosphate polymerase in complex with pyrophosphate

4YEG | pdb_00004yeg

Characterisation of Polyphosphate Kinase 2 from the Intracellular Pathogen Francisella tularensis

5IIG | pdb_00005iig

Structure of the SPX-TTM domain fragment of the yeast inorganic polyphophate polymerase Vtc4 (form A).

5IIQ | pdb_00005iiq

Structure of the SPX-TTM domain fragment of the yeast inorganic polyphophate polymerase Vtc4 (form B).

5IIT | pdb_00005iit

Structure of SPX domain of the yeast inorganic polyphophate polymerase Vtc4 crystallized by carrier-driven crystallization in fusion with the macro domain of human histone macroH2A1.1

5LL0 | pdb_00005ll0

Structure of Polyphosphate Kinase 2 from Francisella tularensis SCHU S4 with polyphosphate

5LLB | pdb_00005llb

Structure of Polyphosphate Kinase 2 from Francisella tularensis with AMPPCH2PPP and polyphosphate

5LLF | pdb_00005llf

Structure of Polyphosphate Kinase 2 mutant D117N from Francisella tularensis with polyphosphate

5LNC | pdb_00005lnc

Structure of SPX domain of the yeast inorganic polyphophate polymerase Vtc4 crystallized by carrier-driven crystallization in fusion with the macro domain of human histone macroH2A1.1

6DZG | pdb_00006dzg

Crystal structure of polyphosphate kinase 2 class I (SMc02148) in complex with ADP

7BMM | pdb_00007bmm

Crystal structure of Polyphosphate Kinase 2 from Deinococcus radiodurans in apo form

7YTJ | pdb_00007ytj

Cryo-EM structure of VTC complex

8I6V | pdb_00008i6v

Cryo-EM structure of the polyphosphate polymerase VTC complex(Vtc4/Vtc3/Vtc1)

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Structure Determination Methodology

Scientific Name of Source Organism

Taxonomy

Experimental Method

Polymer Entity Type

Refinement Resolution (Å)

Release Date

Enzyme Classification Name

Membrane Protein Annotation

Symmetry Type

SCOP Classification

1XDO | pdb_00001xdo

1XDP | pdb_00001xdp

2O8R | pdb_00002o8r

3G3Q | pdb_00003g3q

3G3R | pdb_00003g3r

3G3T | pdb_00003g3t

3G3U | pdb_00003g3u

4YEG | pdb_00004yeg

5IIG | pdb_00005iig

5IIQ | pdb_00005iiq

5IIT | pdb_00005iit

5LL0 | pdb_00005ll0

5LLB | pdb_00005llb

5LLF | pdb_00005llf

5LNC | pdb_00005lnc

6DZG | pdb_00006dzg

7BMM | pdb_00007bmm

7YTJ | pdb_00007ytj

8I6V | pdb_00008i6v