SMTL ID : 3s1f.1

Asp169Glu mutant of maize cytokinin oxidase/dehydrogenase complexed with N6-isopentenyladenine

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 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: 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.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, E.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: ZIP.3 29 PLIP interactions: 29 interactions with chain A Hydrophobic interactions: A:F.43, 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:E.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:E.151 pi-Stacking: A:F.82, A:W.379

1 x ZIP: N-(3-METHYLBUT-2-EN-1-YL)-9H-PURIN-6-AMINE(Non-covalent)

ZIP.3: 13 residues within 4Å: Chain A: E.151, 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 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:W.379, A:L.440, A:L.474 Hydrogen bonds: A:E.363

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

NAG.4: 4 residues within 4Å: Chain A: T.41, N.45, I.46, T.47 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.45 Water bridges: A:D.42, A:I.46 NAG.5: 6 residues within 4Å: Chain A: P.112, P.113, R.114, N.116, G.127, R.219 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:P.113, A:N.116 NAG.6: 2 residues within 4Å: Chain A: N.305, T.307 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.305

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

PEG.7: 5 residues within 4Å: Chain A: L.29, T.31, A.52, Y.78, V.99 No protein-ligand interaction detected (PLIP)

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.8: 9 residues within 4Å: Chain A: N.163, G.209, L.211, F.383, A.426, A.427, T.472, Y.473, H.486 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.163, A:A.427, A:T.472, A:H.486 Water bridges: A:L.474 GOL.9: 5 residues within 4Å: Chain A: W.379, L.380, N.456, L.460, A.475 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.456 GOL.10: 9 residues within 4Å: Chain A: D.42, F.43, R.83, R.85, G.86, H.87, Y.152, E.364, W.373 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.83, A:R.85, A:E.364 GOL.11: 5 residues within 4Å: Chain A: Y.470, H.477, D.482, R.485, H.486 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.470, A:D.482 Water bridges: A:Y.470, A:Y.470 GOL.12: 3 residues within 4Å: Chain A: G.27, R.30, Y.56 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.30 GOL.13: 5 residues within 4Å: Chain A: I.115, N.116, V.117, A.138, R.142 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:V.117, A:V.117, A:A.138 GOL.14: 10 residues within 4Å: Chain A: E.151, R.235, Y.268, E.270, G.271, S.272, E.313, I.411 Ligands: ZIP.3, GOL.15 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.235, A:Y.268, A:S.272, A:S.272 Water bridges: A:E.313, A:R.359 GOL.15: 7 residues within 4Å: Chain A: R.235, T.286, R.359, V.360, E.363 Ligands: ZIP.3, GOL.14 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.235, A:R.359 Water bridges: A:E.363

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