SMTL ID : 3ed1.8 (8 other biounits)

Crystal Structure of Rice GID1 complexed with GA3

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-dimer

Ligands

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

MPD.1: 11 residues within 4Å: Chain A: L.22, N.25, F.26, S.29, Y.30, L.48, D.49, R.50 Chain B: N.25, R.50 Ligands: MPD.7 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:L.22, A:N.25, A:Y.30 Hydrogen bonds: A:R.50, A:R.50, B:R.50 MPD.7: 11 residues within 4Å: Chain A: N.25, R.50 Chain B: L.22, N.25, F.26, S.29, Y.30, L.48, D.49, R.50 Ligands: MPD.1 8 PLIP interactions: 7 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:L.22, B:N.25, B:F.26, B:F.26, B:Y.30 Hydrogen bonds: B:R.50, B:R.50, A:R.50

6 x NO3: NITRATE ION(Non-functional Binders)

NO3.2: 3 residues within 4Å: Chain A: R.34, Q.248, W.252 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.34, A:Q.248 NO3.4: 3 residues within 4Å: Chain A: T.230, D.263, R.264 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.264, A:R.264, A:R.264 NO3.5: 5 residues within 4Å: Chain A: L.22, R.50, I.132, L.329, L.330 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.50 NO3.6: 7 residues within 4Å: Chain A: N.25, S.29, L.48 Chain B: H.18, L.22, R.50 Ligands: PO4.10 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:R.50, B:R.50, A:N.25, A:S.29, A:S.29 NO3.8: 3 residues within 4Å: Chain B: R.34, Q.248, W.252 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.34, B:Q.248 Water bridges: B:R.34 NO3.9: 3 residues within 4Å: Chain B: T.230, D.263, R.264 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.264, B:R.264, B:R.264

2 x GA3: GIBBERELLIN A3(Non-covalent)

GA3.3: 18 residues within 4Å: Chain A: I.23, F.26, Y.30, R.34, G.121, S.122, I.132, Y.133, D.196, S.197, F.244, V.245, D.249, R.250, Y.253, V.325, G.326, Y.328 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:I.23, A:F.26, A:Y.30, A:I.132, A:V.245, A:Y.253 Hydrogen bonds: A:G.121, A:S.197, A:D.249, A:R.250 Water bridges: A:G.326 Salt bridges: A:R.250 GA3.11: 18 residues within 4Å: Chain B: I.23, F.26, Y.30, R.34, G.121, S.122, I.132, Y.133, D.196, S.197, F.244, V.245, D.249, R.250, Y.253, V.325, G.326, Y.328 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:I.23, B:F.26, B:Y.30, B:I.132, B:V.245, B:Y.253 Hydrogen bonds: B:G.121, B:Y.133, B:S.197, B:D.249, B:R.250 Water bridges: B:Y.328 Salt bridges: B:R.250

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

PO4.10: 7 residues within 4Å: Chain A: L.48 Chain B: L.22, R.50, I.132, L.329, L.330 Ligands: NO3.6 3 PLIP interactions: 3 interactions with chain B Water bridges: B:I.132, B:S.135 Salt bridges: B:R.50

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Shimada, A. et al., Structural basis for gibberellin recognition by its receptor GID1. Nature (2008)

Release Date

2008-11-25

Peptides

Gibberellin receptor GID1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Gibberellin receptor GID1

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