SMTL ID : 9jqg.1 (1 other biounit)

Crystal structure of rice DWARF14 in complex with Cyclo(L-Leu-L-Pro)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

monomer

Ligands

1 x 01: (3~{S},8~{a}~{S})-3-(2-methylpropyl)-2,3,6,7,8,8~{a}-hexahydropyrrolo[1,2-a]pyrazine-1,4-dione

01.1: 8 residues within 4Å: Chain A: F.137, V.145, W.156, Y.160, C.192, V.220, S.221 Ligands: BEZ.5 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:F.137, A:V.145, A:W.156

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 5 residues within 4Å: Chain A: D.132, Y.133, H.134, S.225, V.226 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.132, A:H.134 GOL.3: 4 residues within 4Å: Chain A: V.15, R.48, L.87, I.89 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.48, A:L.87 GOL.4: 5 residues within 4Å: Chain A: D.71, H.190, Q.193, T.194, K.197 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.193, A:T.194, A:K.197, A:K.197

1 x BEZ: BENZOIC ACID(Non-covalent)

BEZ.5: 9 residues within 4Å: Chain A: F.29, S.98, F.127, C.192, V.195, F.196, S.221, H.248 Ligands: 01.1 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:F.29, A:F.29, A:F.127, A:V.195 Hydrogen bonds: A:S.221 Water bridges: A:S.98 Salt bridges: A:H.248 pi-Stacking: A:F.196

1 x PDO: 1,3-PROPANDIOL(Non-covalent)

PDO.6: 7 residues within 4Å: Chain A: K.117, P.210, C.211, V.212, R.237, T.238, T.239 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.117, A:R.237, A:T.239, A:T.239 Water bridges: A:R.264

1 x BU1: 1,4-BUTANEDIOL(Non-functional Binders)

BU1.7: 5 residues within 4Å: Chain A: Q.144, A.148, W.156, G.159, Y.160 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.144, A:Q.144, A:W.156 Water bridges: A:G.159

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhang, J. et al., Root microbiota regulates tiller number in rice. Cell (2025)

Release Date

2025-05-21

Peptides

Strigolactone esterase D14: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Strigolactone esterase D14

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