SMTL ID : 6yap.1

Crystal structure of ZmCKO4a in complex with inhibitor 1-(3-Chloro-5-trifluoromethoxy-phenyl)-3-[2-(2-hydroxy-ethyl)-phenyl]-urea

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

monomer

Ligands

4 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.1: 1 residues within 4Å: Chain A: R.404 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.404 EDO.2: 3 residues within 4Å: Chain A: P.220, D.221, R.435 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.435 EDO.8: 3 residues within 4Å: Chain A: W.252, F.357, T.359 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:F.357, A:T.359 EDO.9: 5 residues within 4Å: Chain A: N.219, P.220, D.221, L.222, F.516 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.221, A:L.222

1 x FAD: FLAVIN-ADENINE DINUCLEOTIDE(Covalent)

FAD.3: 35 residues within 4Å: Chain A: F.57, A.95, R.96, G.97, H.98, G.99, H.100, S.101, Q.105, A.106, M.116, G.146, T.169, D.170, Y.171, L.174, S.175, G.177, G.178, T.179, S.181, N.182, G.184, I.185, G.231, G.234, I.235, I.236, W.383, W.389, Y.487, L.488, A.523, Q.526 Ligands: OHZ.4 31 PLIP interactions: 31 interactions with chain A Hydrophobic interactions: A:F.57, A:F.57, A:H.100, A:Y.171, A:Y.171, A:L.174, A:W.383, A:W.389 Hydrogen bonds: A:A.95, A:G.97, A:H.98, A:G.99, A:H.100, A:H.100, A:S.101, A:Q.105, A:D.170, A:Y.171, A:S.175, A:S.175, A:S.181, A:N.182, A:G.184, A:I.185, A:I.185, A:I.236, A:I.236, A:Y.487, A:Q.526 Water bridges: A:S.101 pi-Stacking: A:W.389

1 x OHZ: 1-(3-Chloro-5-trifluoromethoxy-phenyl)-3-[2-(2-hydroxy-ethyl)-phenyl]-urea(Non-covalent)

OHZ.4: 15 residues within 4Å: Chain A: D.170, I.185, E.285, V.370, L.377, W.383, W.389, N.391, L.423, Y.425, L.448, L.452, Y.487, L.488 Ligands: FAD.3 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:V.370, A:V.370, A:W.389, A:L.448, A:L.452, A:Y.487, A:L.488 Hydrogen bonds: A:D.170, A:D.170, A:E.285, A:Y.425

3 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.5: 3 residues within 4Å: Chain A: D.143, R.238, R.240 No protein-ligand interaction detected (PLIP) DMS.6: 2 residues within 4Å: Chain A: H.430, K.431 No protein-ligand interaction detected (PLIP) DMS.7: 3 residues within 4Å: Chain A: L.474, C.477, A.484 1 PLIP interactions: 1 interactions with chain A Water bridges: A:Q.486

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nisler, J. et al., Diphenylurea-derived cytokinin oxidase/dehydrogenase inhibitors for biotechnology and agriculture. J.Exp.Bot. (2021)

Release Date

2020-10-14

Peptides

Cytokinin dehydrogenase 4: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Cytokinin dehydrogenase 4

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