SMTL ID : 3kjm.1

Leu492Ala mutant of Maize cytokinin oxidase/dehydrogenase complexed with phenylurea inhibitor CPPU

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

monomer

Ligands

2 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.1: 6 residues within 4Å: Chain A: P.112, P.113, R.114, N.116, D.125, R.219 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 4 residues within 4Å: Chain A: N.276, Q.277, N.305, A.306 No protein-ligand interaction detected (PLIP)

1 x FAD: FLAVIN-ADENINE DINUCLEOTIDE(Covalent)

FAD.3: 33 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, G.212, G.215, V.216, I.217, W.379, Y.473, S.509, Q.512 Ligands: 245.4 28 PLIP interactions: 28 interactions with chain A Hydrophobic interactions: A:F.43, A:F.43, A:Y.152, A:Y.152, A:L.155, A:W.379, 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: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:Y.473, A:Q.512 Water bridges: A:S.88, A:T.156, A:N.163

1 x 245: 1-(2-chloropyridin-4-yl)-3-phenylurea(Non-covalent)

245.4: 10 residues within 4Å: Chain A: D.151, V.360, W.379, N.381, I.411, S.438, L.440, Y.473 Ligands: FAD.3, GOL.9 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:D.151, A:V.360, A:V.360, A:W.379, A:I.411, A:L.440 Hydrogen bonds: A:D.151, A:D.151

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

NAG.5: 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:T.47 NAG.6: 2 residues within 4Å: Chain A: N.305, T.307 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.305 Water bridges: A:T.307

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 5 residues within 4Å: Chain A: S.178, S.418, M.419, W.420, D.421 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.178, A:D.421 Water bridges: A:K.197 GOL.8: 7 residues within 4Å: Chain A: P.15, W.16, L.20, T.73, W.76, P.77, Y.78 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:P.15 GOL.9: 7 residues within 4Å: Chain A: N.285, T.286, E.363, K.369, L.370 Ligands: 245.4, GOL.10 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.285, A:E.363, A:K.369 Water bridges: A:V.360, A:E.363 GOL.10: 7 residues within 4Å: Chain A: D.282, N.285, T.286, L.370, G.408, P.409 Ligands: GOL.9 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.282, A:D.282, A:N.285, A:G.408 GOL.11: 8 residues within 4Å: Chain A: A.206, D.422, G.423, M.424, S.425, K.491, R.494, F.495 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.423 Water bridges: A:A.206 GOL.12: 7 residues within 4Å: Chain A: Y.470, K.471, T.472, H.477, D.482, R.485, H.486 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:K.471, A:T.472, A:T.472, A:D.482, A:D.482 Water bridges: A:Y.470, A:Y.470, A:K.471 GOL.13: 6 residues within 4Å: Chain A: R.250, L.251, R.255, G.264, P.265, T.338 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:L.251, A:R.255, A:R.255, A:T.338 GOL.14: 5 residues within 4Å: Chain A: L.336, L.339, S.340, Y.341, E.343 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:L.339, A:Y.341 Water bridges: A:Y.341, A:Y.341, A:E.343

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kopecny, D. et al., Phenyl- and benzylurea cytokinins as competitive inhibitors of cytokinin oxidase/dehydrogenase: a structural study. Biochimie (2010)

Release Date

2010-05-26

Peptides

Cytokinin dehydrogenase 1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Cytokinin dehydrogenase 1

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