SMTL ID : 3s1d.1

Glu381Ser mutant of maize cytokinin oxidase/dehydrogenase complexed with N6-isopentenyladenosine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

monomer

Ligands

1 x FAD: FLAVIN-ADENINE DINUCLEOTIDE(Covalent)

FAD.1: 36 residues within 4Å: Chain A: F.43, F.82, R.83, G.84, R.85, G.86, H.87, S.88, Q.92, A.93, M.103, G.128, T.150, D.151, Y.152, L.155, T.156, G.158, G.159, T.160, S.162, N.163, G.165, I.166, L.211, G.212, G.215, V.216, I.217, W.373, W.379, Y.473, L.474, S.509, Q.512 Ligands: ZIR.2 26 PLIP interactions: 26 interactions with chain A Hydrophobic interactions: A:F.43, A:Y.152, A:Y.152, A:L.155, A:W.373, A:W.379 Hydrogen bonds: A:F.82, A:G.84, A:R.85, A:G.86, A:H.87, A:H.87, A:S.88, A:S.88, A:D.151, A:T.156, A:S.162, A:N.163, A:G.165, A:I.166, A:I.166, A:I.217, A:I.217, A:S.509, A:Q.512 pi-Stacking: A:W.379

1 x ZIR: N-(3-methylbut-2-en-1-yl)adenosine(Non-covalent)

ZIR.2: 14 residues within 4Å: Chain A: D.151, R.235, N.285, T.286, V.360, S.363, W.379, N.381, P.409, I.411, S.438, L.440, L.474 Ligands: FAD.1 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:W.379, A:L.440, A:L.474 Hydrogen bonds: A:D.151, A:D.151, A:R.235, A:S.363, A:S.363 Water bridges: A:S.272

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 4 residues within 4Å: Chain A: A.280, V.294, A.295, V.298 1 PLIP interactions: 1 interactions with chain A Water bridges: A:A.295 GOL.4: 4 residues within 4Å: Chain A: L.336, G.337, L.339, Y.341 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.341 GOL.6: 6 residues within 4Å: Chain A: W.16, L.29, T.31, A.52, A.53, Y.78 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:A.52 GOL.7: 5 residues within 4Å: Chain A: S.178, S.418, M.419, W.420, D.421 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:M.419 Water bridges: A:D.422 GOL.8: 3 residues within 4Å: Chain A: Q.469, Y.470, R.485 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.470, A:R.485 Water bridges: A:I.468, A:K.471

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.5: 2 residues within 4Å: Chain A: R.394, K.398 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.394, A:K.398

3 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.9: 4 residues within 4Å: Chain A: T.41, N.45, I.46, T.47 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.45 Water bridges: A:I.46 NAG.10: 4 residues within 4Å: Chain A: N.276, Q.277, N.305, A.306 5 PLIP interactions: 5 interactions with chain A Water bridges: A:N.276, A:N.276, A:N.276, A:N.305, A:A.306 NAG.11: 2 residues within 4Å: Chain A: N.305, T.307 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.305

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kopecny, D. et al., Kinetic and structural investigation of the cytokinin oxidase/dehydrogenase active site. Febs J. (2016)

Release Date

2012-05-23

Peptides

Cytokinin dehydrogenase 1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Cytokinin dehydrogenase 1