SMTL ID : 7ekd.1

Crystal structure of gibberellin 3-oxidase 2 (GA3ox2) in rice

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

monomer

Ligands

4 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.1: 3 residues within 4Å: Chain A: H.273, H.281 Ligands: PO4.3 6 PLIP interactions: 6 interactions with chain A Water bridges: A:H.273, A:H.273, A:G.278, A:H.281 Salt bridges: A:H.273, A:H.281 PO4.2: 5 residues within 4Å: Chain A: S.137, H.165, R.169, T.204, A.205 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:A.205, A:A.205 Water bridges: A:S.137 Salt bridges: A:H.165, A:R.169 PO4.3: 5 residues within 4Å: Chain A: F.247, R.249, H.281, Y.284 Ligands: PO4.1 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.249 Water bridges: A:S.282 Salt bridges: A:H.281 PO4.4: 3 residues within 4Å: Chain A: R.202, A.308, E.309 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.309 Salt bridges: A:R.202

1 x AKG: 2-OXOGLUTARIC ACID(Non-covalent)

AKG.5: 12 residues within 4Å: Chain A: N.210, Y.212, L.224, H.227, D.229, V.236, L.244, H.285, R.295, S.297, F.301 Ligands: J5X.7 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:L.224, A:L.244 Hydrogen bonds: A:N.210, A:Y.212, A:D.229, A:S.297 Water bridges: A:N.267 Salt bridges: A:H.227, A:R.295

1 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.6: 7 residues within 4Å: Chain A: P.118, F.122, M.334, R.337, K.338, F.341 Ligands: J5X.7 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:R.337, A:K.338, A:F.341 Hydrogen bonds: A:S.230, A:R.337

1 x J5X: Gibberellin A9(Non-covalent)

J5X.7: 12 residues within 4Å: Chain A: P.117, P.118, I.119, T.206, H.227, D.229, S.230, F.301, M.334, R.337 Ligands: AKG.5, MPD.6 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:P.117, A:T.206, A:F.301, A:F.301 Hydrogen bonds: A:I.119, A:S.230 Water bridges: A:G.231, A:G.231 Salt bridges: A:R.337

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kawai, K. et al., Evolutionary alterations in gene expression and enzymatic activities of gibberellin 3-oxidase 1 in Oryza. Commun Biol (2022)

Release Date

2022-02-16

Peptides

Gibberellin 3-beta-dioxygenase 2: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Gibberellin 3-beta-dioxygenase 2