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234,785 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Gene Name = "GIP2"

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Search Summary

This query matches 15 Structures.

Refinements

Structure Determination Methodology

experimental (15)

Scientific Name of Source Organism

Arabidopsis thaliana (15)

Taxonomy

Eukaryota (15)

Experimental Method

	X-RAY DIFFRACTION (14)
	ELECTRON MICROSCOPY (1)

Polymer Entity Type

Protein (15)

Refinement Resolution (Å)

	1.5 - 2.0 (7)
	2.0 - 2.5 (4)
	2.5 - 3.0 (3)
	3.0 - 3.5 (1)

Release Date

	2015 - 2019 (10)
	2020 - 2024 (5)

Enzyme Classification Name

Lyases (15)

Symmetry Type

	Dihedral (13)
	Cyclic (2)

SCOP Classification

Alpha and beta proteins (a/b) (10)

AllSelected

1 to 15 of 15 Structures

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Explore in 3D

5K2Z \| pdb_00005k2z	Download File View File

PDX1.3-adduct (Arabidopsis)

Robinson, G.C., Kaufmann, M., Roux, C., Fitzpatrick, T.B.

(2016) Proc Natl Acad Sci U S A 113: E5821-E5829

Released	2016-10-05
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Arabidopsis thaliana
Macromolecule	Pyridoxal 5'-phosphate synthase subunit PDX1.3 (protein)
Unique Ligands	6R3, CL, EDO, SO4

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5K3V \| pdb_00005k3v	Download File View File

apo-PDX1.3 (Arabidopsis)

Robinson, G.C., Kaufmann, M., Roux, C., Fitzpatrick, T.B.

(2016) Proc Natl Acad Sci U S A 113: E5821-E5829

Released	2016-10-05
Method	X-RAY DIFFRACTION 1.9 Å
Organisms	Arabidopsis thaliana
Macromolecule	Pyridoxal 5'-phosphate synthase subunit PDX1.3 (protein)
Unique Ligands	CL, EDO, SO4

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5LNR \| pdb_00005lnr	Download File View File

Crystal structure of Arabidopsis thaliana Pdx1-PLP complex

Rodrigues, M.J., Windeisen, V., Zhang, Y., Guedez, G., Weber, S., Strohmeier, M., Hanes, J.W., Royant, A., Evans, G., Sinning, I., Ealick, S.E., Begley, T.P., Tews, I.

(2017) Nat Chem Biol 13: 290-294

Released	2017-01-18
Method	X-RAY DIFFRACTION 1.61 Å
Organisms	Arabidopsis thaliana
Macromolecule	Pyridoxal 5'-phosphate synthase subunit PDX1.3 (protein)
Unique Ligands	GOL, PLP

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5LNS \| pdb_00005lns	Download File View File

Crystal structure of Arabidopsis thaliana Pdx1-R5P complex

Rodrigues, M.J., Windeisen, V., Zhang, Y., Guedez, G., Weber, S., Strohmeier, M., Hanes, J.W., Royant, A., Evans, G., Sinning, I., Ealick, S.E., Begley, T.P., Tews, I.

(2017) Nat Chem Biol 13: 290-294

Released	2017-01-18
Method	X-RAY DIFFRACTION 1.91 Å
Organisms	Arabidopsis thaliana
Macromolecule	Pyridoxal 5'-phosphate synthase subunit PDX1.3 (protein)
Unique Ligands	5RP, PO4

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5LNU \| pdb_00005lnu	Download File View File

Crystal structure of Arabidopsis thaliana Pdx1-I320 complex

Rodrigues, M.J., Windeisen, V., Zhang, Y., Guedez, G., Weber, S., Strohmeier, M., Hanes, J.W., Royant, A., Evans, G., Sinning, I., Ealick, S.E., Begley, T.P., Tews, I.

(2017) Nat Chem Biol 13: 290-294

Released	2017-01-18
Method	X-RAY DIFFRACTION 1.73 Å
Organisms	Arabidopsis thaliana
Macromolecule	Pyridoxal 5'-phosphate synthase subunit PDX1.3 (protein)
Unique Ligands	KIK, PO4, SO4

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5LNV \| pdb_00005lnv	Download File View File

Crystal structure of Arabidopsis thaliana Pdx1-I320 complex from multiple crystals

Rodrigues, M.J., Windeisen, V., Zhang, Y., Guedez, G., Weber, S., Strohmeier, M., Hanes, J.W., Royant, A., Evans, G., Sinning, I., Ealick, S.E., Begley, T.P., Tews, I.

(2017) Nat Chem Biol 13: 290-294

Released	2017-01-18
Method	X-RAY DIFFRACTION 2.24 Å
Organisms	Arabidopsis thaliana
Macromolecule	Pyridoxal 5'-phosphate synthase subunit PDX1.3 (protein)
Unique Ligands	KIK, PO4, SO4

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5LNW \| pdb_00005lnw	Download File View File

Crystal structure of Arabidopsis thaliana Pdx1-I320-G3P complex

Rodrigues, M.J., Windeisen, V., Zhang, Y., Guedez, G., Weber, S., Strohmeier, M., Hanes, J.W., Royant, A., Evans, G., Sinning, I., Ealick, S.E., Begley, T.P., Tews, I.

(2017) Nat Chem Biol 13: 290-294

Released	2017-01-18
Method	X-RAY DIFFRACTION 1.9 Å
Organisms	Arabidopsis thaliana
Macromolecule	Pyridoxal 5'-phosphate synthase subunit PDX1.3 (protein)
Unique Ligands	GOL, HG3, K8P, RP5

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6HX3 \| pdb_00006hx3	Download File View File

PDX1.2/PDX1.3 complex

Robinson, G.C., Kaufmann, M., Roux, C., Martinez-Font, J., Hothorn, M., Thore, S., Fitzpatrick, T.B.

(2019) Acta Crystallogr D Struct Biol 75: 400-415

Released	2019-04-17
Method	X-RAY DIFFRACTION 2 Å
Organisms	Arabidopsis thaliana
Macromolecule	Pyridoxal 5'-phosphate synthase subunit PDX1.3 (protein) Pyridoxal 5'-phosphate synthase-like subunit PDX1.2 (protein)
Unique Ligands	SO4

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6HXG \| pdb_00006hxg	Download File View File

PDX1.2/PDX1.3 complex (intermediate)

Robinson, G.C., Kaufmann, M., Roux, C., Martinez-Font, J., Hothorn, M., Thore, S., Fitzpatrick, T.B.

(2019) Acta Crystallogr D Struct Biol 75: 400-415

Released	2019-04-17
Method	X-RAY DIFFRACTION 1.9 Å
Organisms	Arabidopsis thaliana
Macromolecule	Pyridoxal 5'-phosphate synthase subunit PDX1.3 (protein) Pyridoxal 5'-phosphate synthase-like subunit PDX1.2 (protein)
Unique Ligands	SO4

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6HYE \| pdb_00006hye	Download File View File

PDX1.2/PDX1.3 complex (PDX1.3:K97A)

Robinson, G.C., Kaufmann, M., Roux, C., Martinez-Font, J., Hothorn, M., Thore, S., Fitzpatrick, T.B.

(2019) Acta Crystallogr D Struct Biol 75: 400-415

Released	2019-04-24
Method	X-RAY DIFFRACTION 2.53 Å
Organisms	Arabidopsis thaliana
Macromolecule	Pyridoxal 5'-phosphate synthase subunit PDX1.3 (protein) Pyridoxal 5'-phosphate synthase-like subunit PDX1.2 (protein)
Unique Ligands	SO4

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7LB6 \| pdb_00007lb6	Download File View File

PDX1.2/PDX1.3 co-expression complex

Novikova, I.V., Evans, J.E.

(2021) ACS Chem Biol 16: 2315-2325

Released	2021-09-22
Method	ELECTRON MICROSCOPY 3.16 Å
Organisms	Arabidopsis thaliana
Macromolecule	Pyridoxal 5'-phosphate synthase subunit PDX1.3 (protein) Pyridoxal 5'-phosphate synthase-like subunit PDX1.2 (protein)

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7NHE \| pdb_00007nhe	Download File View File

Crystal structure of Arabidopsis thaliana Pdx1K166R-I333 complex

Rodrigues, M.J., Zhang, Y., Bolton, R., Evans, G., Giri, N., Royant, A., Begley, T., Ealick, S.E., Tews, I.

(2022) RSC Chem Biol 3: 227-230

Released	2021-12-22
Method	X-RAY DIFFRACTION 2.23 Å
Organisms	Arabidopsis thaliana
Macromolecule	Pyridoxal 5'-phosphate synthase subunit PDX1.3 (protein)
Unique Ligands	KPR, PO4

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7NHF \| pdb_00007nhf	Download File View File

Crystal structure of Arabidopsis thaliana Pdx1K166R

Rodrigues, M.J., Zhang, Y., Bolton, R., Evans, G., Giri, N., Royant, A., Begley, T., Ealick, S.E., Tews, I.

(2022) RSC Chem Biol 3: 227-230

Released	2021-12-22
Method	X-RAY DIFFRACTION 2.35 Å
Organisms	Arabidopsis thaliana
Macromolecule	Pyridoxal 5'-phosphate synthase subunit PDX1.3 (protein)
Unique Ligands	PO4

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8S2W \| pdb_00008s2w	Download File View File

SSX structure of Arabidopsis thaliana Pdx1.3 grown in seeded batch conditions

Stubbs, J., Tews, I., Maly, M.

(2024) IUCrJ 11: 237-248

Released	2024-02-28
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Arabidopsis thaliana
Macromolecule	Pyridoxal 5'-phosphate synthase subunit PDX1.3 (protein)
Unique Ligands	PO4

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8S2X \| pdb_00008s2x	Download File View File

SSX structure of Arabidopsis thaliana Pdx1.3 grown in microfluidic droplets

Stubbs, J., Tews, I., Maly, M.

(2024) IUCrJ 11: 237-248

Released	2024-02-28
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Arabidopsis thaliana
Macromolecule	Pyridoxal 5'-phosphate synthase subunit PDX1.3 (protein)
Unique Ligands	CIT, PO4

1 to 15 of 15 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.

5K2Z | pdb_00005k2z

PDX1.3-adduct (Arabidopsis)

5K3V | pdb_00005k3v

apo-PDX1.3 (Arabidopsis)

5LNR | pdb_00005lnr

Crystal structure of Arabidopsis thaliana Pdx1-PLP complex

5LNS | pdb_00005lns

Crystal structure of Arabidopsis thaliana Pdx1-R5P complex

5LNU | pdb_00005lnu

Crystal structure of Arabidopsis thaliana Pdx1-I320 complex

5LNV | pdb_00005lnv

Crystal structure of Arabidopsis thaliana Pdx1-I320 complex from multiple crystals

5LNW | pdb_00005lnw

Crystal structure of Arabidopsis thaliana Pdx1-I320-G3P complex

6HX3 | pdb_00006hx3

PDX1.2/PDX1.3 complex

6HXG | pdb_00006hxg

PDX1.2/PDX1.3 complex (intermediate)

6HYE | pdb_00006hye

PDX1.2/PDX1.3 complex (PDX1.3:K97A)

7LB6 | pdb_00007lb6

PDX1.2/PDX1.3 co-expression complex

7NHE | pdb_00007nhe

Crystal structure of Arabidopsis thaliana Pdx1K166R-I333 complex

7NHF | pdb_00007nhf

Crystal structure of Arabidopsis thaliana Pdx1K166R

8S2W | pdb_00008s2w

SSX structure of Arabidopsis thaliana Pdx1.3 grown in seeded batch conditions

8S2X | pdb_00008s2x

SSX structure of Arabidopsis thaliana Pdx1.3 grown in microfluidic droplets

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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

Symmetry Type

SCOP Classification

5K2Z | pdb_00005k2z

5K3V | pdb_00005k3v

5LNR | pdb_00005lnr

5LNS | pdb_00005lns

5LNU | pdb_00005lnu

5LNV | pdb_00005lnv

5LNW | pdb_00005lnw

6HX3 | pdb_00006hx3

6HXG | pdb_00006hxg

6HYE | pdb_00006hye

7LB6 | pdb_00007lb6

7NHE | pdb_00007nhe

7NHF | pdb_00007nhf

8S2W | pdb_00008s2w

8S2X | pdb_00008s2x