SMTL ID : 3s1c.1

Maize cytokinin oxidase/dehydrogenase complexed with N6-isopentenyladenosine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.09 Å

Oligo State

monomer

Ligands

1 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: 5 residues within 4Å: Chain A: N.276, Q.277, N.305, A.306, T.307 No protein-ligand interaction detected (PLIP)

1 x FAD: FLAVIN-ADENINE DINUCLEOTIDE(Covalent)

FAD.2: 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.3 28 PLIP interactions: 28 interactions with chain A Hydrophobic interactions: A:F.43, A:H.87, 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: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 Water bridges: A:H.87 pi-Stacking: A:F.82, A:W.379

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

ZIR.3: 17 residues within 4Å: Chain A: D.151, R.235, N.285, T.286, V.360, E.363, W.379, N.381, P.409, I.411, S.438, L.440, L.474 Ligands: FAD.2, GOL.14, GOL.15, 15P.19 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:W.379, A:L.474 Hydrogen bonds: A:D.151, A:D.151, A:R.235, A:E.363

14 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 7 residues within 4Å: Chain A: F.43, R.83, R.85, G.86, H.87, W.373, R.374 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.83, A:R.85, A:R.374 GOL.5: 4 residues within 4Å: Chain A: R.172, H.173, E.225, S.267 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.173, A:S.267 Water bridges: A:N.317 GOL.6: 5 residues within 4Å: Chain A: A.280, V.294, A.295, V.298 Ligands: GOL.11 1 PLIP interactions: 1 interactions with chain A Water bridges: A:A.295 GOL.7: 3 residues within 4Å: Chain A: A.242, A.246 Ligands: PEG.22 No protein-ligand interaction detected (PLIP) GOL.8: 6 residues within 4Å: Chain A: S.178, S.418, M.419, W.420, D.421 Ligands: GOL.16 2 PLIP interactions: 2 interactions with chain A Water bridges: A:D.421, A:D.421 GOL.9: 4 residues within 4Å: Chain A: R.349, D.350, V.351 Ligands: GOL.12 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.349, A:R.349, A:D.350 Water bridges: A:D.350 GOL.10: 3 residues within 4Å: Chain A: A.299, G.302, E.303 2 PLIP interactions: 2 interactions with chain A Water bridges: A:E.303, A:E.303 GOL.11: 2 residues within 4Å: Chain A: A.295 Ligands: GOL.6 1 PLIP interactions: 1 interactions with chain A Water bridges: A:D.291 GOL.12: 5 residues within 4Å: Chain A: R.232, Q.348, R.349, D.350 Ligands: GOL.9 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.348 Water bridges: A:R.232 GOL.13: 1 residues within 4Å: Chain A: R.296 1 PLIP interactions: 1 interactions with chain A Water bridges: A:R.296 GOL.14: 6 residues within 4Å: Chain A: D.282, N.285, T.286, E.363 Ligands: ZIR.3, GOL.15 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.285 GOL.15: 8 residues within 4Å: Chain A: V.360, E.363, L.367, W.373, P.409, S.442 Ligands: ZIR.3, GOL.14 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.442, A:S.442 GOL.16: 5 residues within 4Å: Chain A: R.147, S.178, L.181, A.223 Ligands: GOL.8 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.147 Water bridges: A:N.179, A:V.180 GOL.17: 7 residues within 4Å: Chain A: N.163, L.211, T.472, Y.473, L.474, A.475, H.486 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:N.163, A:T.472, A:L.474, A:A.475, A:A.475 Water bridges: A:N.163, A:A.427, A:T.472, A:H.486, A:Q.512

4 x 15P: POLYETHYLENE GLYCOL (N=34)(Non-functional Binders)

15P.18: 4 residues within 4Å: Chain A: R.304, V.342, E.343, F.345 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.304, A:E.343 15P.19: 11 residues within 4Å: Chain A: D.151, W.233, R.235, Y.268, E.270, T.286, F.288, E.313, R.349, R.359 Ligands: ZIR.3 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.151, A:R.235, A:Y.268, A:R.359 Water bridges: A:E.313 15P.20: 2 residues within 4Å: Chain A: R.394, K.398 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.398 Water bridges: A:F.241, A:D.393 15P.21: 6 residues within 4Å: Chain A: F.288, D.293, A.346, F.347, Q.348, R.349 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.348, A:Q.348

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

PEG.22: 6 residues within 4Å: Chain A: A.242, A.246, E.249, R.250, R.386 Ligands: GOL.7 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.242 Water bridges: A:S.245 PEG.23: 6 residues within 4Å: Chain A: I.133, R.137, L.140, A.354, A.355, D.358 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.137 PEG.24: 7 residues within 4Å: Chain A: W.16, L.29, A.52, A.53, W.76, Y.78, V.99 No protein-ligand interaction detected (PLIP) PEG.25: 5 residues within 4Å: Chain A: N.285, G.287, E.363, A.366, L.367 No protein-ligand interaction detected (PLIP)

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

NAG.26: 5 residues within 4Å: Chain A: T.41, N.45, I.46, T.47, S.48 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.45 Water bridges: A:I.46 NAG.27: 2 residues within 4Å: Chain A: N.305, T.307 No protein-ligand interaction detected (PLIP)

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

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