RCSB PDB: Search

8J9F \| pdb_00008j9f	Download File View File

Structure of STG-hydrolyzing beta-glucosidase 1 (PSTG1)

Yanai, T., Imaizumi, R., Takahashi, Y., Katsumura, E., Yamamoto, M., Nakayama, T., Yamashita, S., Takeshita, K., Sakai, N., Matsuura, H.

(2023) J Biochem 174: 335-344

Released	2024-04-10
Method	X-RAY DIFFRACTION 2.85 Å
Organisms	Paenibacillus relictisesami
Macromolecule	Beta-glucosidase (protein)
Unique Ligands	GOL

Explore in 3D

8JRD \| pdb_00008jrd	Download File View File

Chalcone synthase from Glycine max (L.) Merr (soybean) complexed with naringenin and coenzyme A

Waki, T., Imaizumi, R., Nakata, S., Yanai, T., Takeshita, K., Sakai, N., Kataoka, K., Yamamoto, M., Nakayama, T., Yamashita, S.

(2024) Biochem Biophys Res Commun 718: 150080-150080

Released	2024-06-19
Method	X-RAY DIFFRACTION 1.83 Å
Organisms	Glycine max
Macromolecule	chalcone synthase (protein)
Unique Ligands	COA, EDO, NAR, PEG, PGE

Explore in 3D

8KGA \| pdb_00008kga	Download File View File

SlNDPS1-AtcPT4 Chimera

Suenaga-Hiromori, M., Ishii, T., Imaizumi, R., Takeshita, K., Yanai, T., Matsuura, H., Sakai, N., Yamaguchi, H., Yanbe, F., Waki, T., Tozawa, Y., Miyagi-Inoue, Y., Yamamoto, M., Kataoka, K., Nakayama, T., Yamashita, S., Takahashi, S.

To be published

Released	2024-08-21
Method	X-RAY DIFFRACTION 2.182 Å
Organisms	Arabidopsis thaliana Solanum lycopersicum
Macromolecule	Dimethylallylcistransferase CPT1, chloroplastic,Dehydrodolichyl diphosphate synthase 2 (protein)
Unique Ligands	EDO, MLI, PEG

Explore in 3D

8KGB \| pdb_00008kgb	Download File View File

SlNDPS1-AtcPT4 Chimera complexed with GSPP, Mg2+, and IPP

Suenaga-Hiromori, M., Ishii, T., Imaizumi, R., Takeshita, K., Yanai, T., Matsuura, H., Sakai, N., Yamaguchi, H., Yanbe, F., Waki, T., Tozawa, Y., Miyagi-Inoue, Y., Yamamoto, M., Kataoka, K., Nakayama, T., Yamashita, S., Takahashi, S.

To be published

Released	2024-08-21
Method	X-RAY DIFFRACTION 2.32 Å
Organisms	Arabidopsis thaliana Solanum lycopersicum
Macromolecule	Dimethylallylcistransferase CPT1, chloroplastic,Dehydrodolichyl diphosphate synthase 2 (protein)
Unique Ligands	GST, IPE, MG

Explore in 3D

8X35 \| pdb_00008x35	Download File View File

Neryl diphosphate synthase from Solanum lycopersicum complexed with DMSAPP, IPP, and magnesium ion (form A)

Imaizumi, R., Matsuura, H., Yanai, T., Takeshita, K., Misawa, S., Yamaguchi, H., Sakai, N., Miyagi-Inoue, Y., Suenaga-Hiromori, M., Kataoka, K., Nakayama, T., Yamamoto, M., Takahashi, S., Yamashita, S.

(2024) Chembiochem 25: e202300796-e202300796

Released	2024-02-07
Method	X-RAY DIFFRACTION 1.92 Å
Organisms	Solanum lycopersicum
Macromolecule	Neryl diphosphate synthase 1 (protein)
Unique Ligands	DPO, DST, EDO, IPE, MG, PEG

Explore in 3D

8X36 \| pdb_00008x36	Download File View File

Neryl diphosphate synthase from Solanum lycopersicum complexed with DMSAPP, IPP, and magnesium ion (form B)

Imaizumi, R., Matsuura, H., Yanai, T., Takeshita, K., Misawa, S., Yamaguchi, H., Sakai, N., Miyagi-Inoue, Y., Suenaga-Hiromori, M., Kataoka, K., Nakayama, T., Yamamoto, M., Takahashi, S., Yamashita, S.

(2024) Chembiochem 25: e202300796-e202300796

Released	2024-02-07
Method	X-RAY DIFFRACTION 2.28 Å
Organisms	Solanum lycopersicum
Macromolecule	Neryl-diphosphate synthase 1 (protein)
Unique Ligands	DST, IPE, MG

Explore in 3D

8X37 \| pdb_00008x37	Download File View File

Neryl diphosphate synthase from Solanum lycopersicum complexed with DMSAPP

Imaizumi, R., Matsuura, H., Yanai, T., Takeshita, K., Misawa, S., Yamaguchi, H., Sakai, N., Miyagi-Inoue, Y., Suenaga-Hiromori, M., Kataoka, K., Nakayama, T., Yamamoto, M., Takahashi, S., Yamashita, S.

(2024) Chembiochem 25: e202300796-e202300796

Released	2024-02-07
Method	X-RAY DIFFRACTION 1.98 Å
Organisms	Solanum lycopersicum
Macromolecule	Neryl-diphosphate synthase 1 (protein)
Unique Ligands	DST, MG

8J9F | pdb_00008j9f

Structure of STG-hydrolyzing beta-glucosidase 1 (PSTG1)

8JRD | pdb_00008jrd

Chalcone synthase from Glycine max (L.) Merr (soybean) complexed with naringenin and coenzyme A

8KGA | pdb_00008kga

SlNDPS1-AtcPT4 Chimera

8KGB | pdb_00008kgb

SlNDPS1-AtcPT4 Chimera complexed with GSPP, Mg2+, and IPP

8X35 | pdb_00008x35

Neryl diphosphate synthase from Solanum lycopersicum complexed with DMSAPP, IPP, and magnesium ion (form A)

8X36 | pdb_00008x36

Neryl diphosphate synthase from Solanum lycopersicum complexed with DMSAPP, IPP, and magnesium ion (form B)

8X37 | pdb_00008x37

Neryl diphosphate synthase from Solanum lycopersicum complexed with DMSAPP

Prepare Data

Validate Data

Deposit Data

Help and Resources

Structure Determination Methodology

Scientific Name of Source Organism

Taxonomy

Experimental Method

Polymer Entity Type

Refinement Resolution (Å)

Release Date

Enzyme Classification Name

Symmetry Type

8J9F | pdb_00008j9f

Structure of STG-hydrolyzing beta-glucosidase 1 (PSTG1)

8JRD | pdb_00008jrd

Chalcone synthase from Glycine max (L.) Merr (soybean) complexed with naringenin and coenzyme A

8KGA | pdb_00008kga

SlNDPS1-AtcPT4 Chimera

8KGB | pdb_00008kgb

SlNDPS1-AtcPT4 Chimera complexed with GSPP, Mg2+, and IPP

8X35 | pdb_00008x35

Neryl diphosphate synthase from Solanum lycopersicum complexed with DMSAPP, IPP, and magnesium ion (form A)

8X36 | pdb_00008x36

Neryl diphosphate synthase from Solanum lycopersicum complexed with DMSAPP, IPP, and magnesium ion (form B)

8X37 | pdb_00008x37

Neryl diphosphate synthase from Solanum lycopersicum complexed with DMSAPP