SMTL ID : 5mog.1

Oryza sativa phytoene desaturase inhibited by norflurazon

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.77 Å

Oligo State

homo-pentamer

Ligands

5 x FAD: FLAVIN-ADENINE DINUCLEOTIDE(Non-covalent)

FAD.1: 36 residues within 4Å: Chain A: G.24, G.26, L.27, A.28, L.46, E.47, A.48, R.49, G.53, G.54, K.55, I.56, T.69, G.70, L.71, H.72, I.73, Y.78, F.196, S.253, R.254, I.255, A.285, T.286, P.287, I.290, L.294, V.316, V.418, G.443, D.444, A.452, S.453, M.454, A.457 Ligands: NRF.2 24 PLIP interactions: 24 interactions with chain A Hydrophobic interactions: A:F.196, A:V.316, A:V.316 Hydrogen bonds: A:A.28, A:A.48, A:R.49, A:G.53, A:K.55, A:H.72, A:I.73, A:I.73, A:I.255, A:I.255, A:D.444, A:D.444, A:A.452, A:M.454 Water bridges: A:G.26, A:G.29 Salt bridges: A:K.55, A:K.55 pi-Stacking: A:F.196 pi-Cation interactions: A:H.72, A:H.72 FAD.6: 36 residues within 4Å: Chain B: G.24, G.26, L.27, A.28, L.46, E.47, A.48, R.49, G.53, G.54, K.55, I.56, T.69, G.70, L.71, H.72, I.73, Y.78, F.196, S.253, R.254, I.255, A.285, T.286, P.287, I.290, L.294, V.316, V.418, G.443, D.444, A.452, S.453, M.454, A.457 Ligands: NRF.7 26 PLIP interactions: 26 interactions with chain B Hydrophobic interactions: B:F.196, B:V.316, B:V.316 Hydrogen bonds: B:A.28, B:A.48, B:R.49, B:K.55, B:H.72, B:I.73, B:I.73, B:I.255, B:I.255, B:D.444, B:D.444, B:A.452, B:M.454 Water bridges: B:G.26, B:G.29, B:R.49, B:R.49, B:K.55, B:K.55 Salt bridges: B:K.55, B:K.55 pi-Cation interactions: B:H.72, B:H.72 FAD.13: 36 residues within 4Å: Chain C: G.24, G.26, L.27, A.28, L.46, E.47, A.48, R.49, G.53, G.54, K.55, I.56, T.69, G.70, L.71, H.72, I.73, Y.78, F.196, S.253, R.254, I.255, A.285, T.286, P.287, I.290, L.294, V.316, V.418, G.443, D.444, A.452, S.453, M.454, A.457 Ligands: NRF.14 21 PLIP interactions: 21 interactions with chain C Hydrophobic interactions: C:F.196, C:V.316, C:V.316 Hydrogen bonds: C:A.28, C:A.48, C:R.49, C:K.55, C:H.72, C:I.73, C:I.73, C:I.255, C:I.255, C:T.286, C:D.444, C:D.444, C:A.452, C:M.454 Salt bridges: C:K.55, C:K.55 pi-Cation interactions: C:H.72, C:H.72 FAD.15: 36 residues within 4Å: Chain D: G.24, G.26, L.27, A.28, L.46, E.47, A.48, R.49, G.53, G.54, K.55, I.56, T.69, G.70, L.71, H.72, I.73, Y.78, F.196, S.253, R.254, I.255, A.285, T.286, P.287, I.290, L.294, V.316, V.418, G.443, D.444, A.452, S.453, M.454, A.457 Ligands: NRF.16 24 PLIP interactions: 24 interactions with chain D Hydrophobic interactions: D:F.196, D:V.316, D:V.316 Hydrogen bonds: D:A.28, D:A.48, D:R.49, D:K.55, D:H.72, D:I.73, D:I.73, D:I.255, D:I.255, D:T.286, D:D.444, D:A.452, D:M.454 Water bridges: D:G.26, D:G.29, D:K.55, D:K.55 Salt bridges: D:K.55, D:K.55 pi-Cation interactions: D:H.72, D:H.72 FAD.21: 35 residues within 4Å: Chain E: G.24, G.26, L.27, A.28, L.46, E.47, A.48, R.49, G.53, G.54, K.55, I.56, T.69, G.70, L.71, H.72, I.73, Y.78, F.196, S.253, R.254, I.255, A.285, T.286, P.287, I.290, V.316, V.418, G.443, D.444, A.452, S.453, M.454, A.457 Ligands: NRF.22 24 PLIP interactions: 24 interactions with chain E Hydrophobic interactions: E:F.196, E:V.316, E:V.316 Hydrogen bonds: E:A.28, E:A.48, E:R.49, E:G.53, E:K.55, E:H.72, E:I.73, E:I.73, E:Y.78, E:I.255, E:I.255, E:T.286, E:D.444, E:A.452, E:M.454 Water bridges: E:L.27, E:L.27 Salt bridges: E:K.55, E:K.55 pi-Cation interactions: E:H.72, E:H.72

5 x NRF: Norflurazon(Non-covalent)

NRF.2: 12 residues within 4Å: Chain A: F.75, Y.78, M.190, A.193, L.194, F.196, R.213, L.334, F.336, A.452, S.453 Ligands: FAD.1 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:A.193, A:L.194, A:L.334, A:F.336 Hydrogen bonds: A:Y.78, A:R.213, A:R.213 pi-Stacking: A:F.75 NRF.7: 12 residues within 4Å: Chain B: F.75, Y.78, M.190, A.193, L.194, F.196, R.213, L.334, F.336, A.452, S.453 Ligands: FAD.6 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:A.193, B:L.194, B:L.334, B:F.336 Hydrogen bonds: B:Y.78, B:R.213, B:R.213 pi-Stacking: B:F.75 NRF.14: 12 residues within 4Å: Chain C: F.75, Y.78, M.190, A.193, L.194, F.196, R.213, L.334, F.336, A.452, S.453 Ligands: FAD.13 9 PLIP interactions: 9 interactions with chain C Hydrophobic interactions: C:A.193, C:L.194, C:L.334, C:F.336 Hydrogen bonds: C:Y.78, C:R.213, C:R.213 Water bridges: C:A.452 pi-Stacking: C:F.75 NRF.16: 12 residues within 4Å: Chain D: F.75, Y.78, M.190, A.193, L.194, F.196, R.213, L.334, F.336, A.452, S.453 Ligands: FAD.15 8 PLIP interactions: 8 interactions with chain D Hydrophobic interactions: D:A.193, D:L.194, D:L.334, D:F.336 Hydrogen bonds: D:Y.78, D:R.213, D:R.213 pi-Stacking: D:F.75 NRF.22: 12 residues within 4Å: Chain E: F.75, Y.78, M.190, A.193, L.194, F.196, R.213, L.334, F.336, A.452, S.453 Ligands: FAD.21 7 PLIP interactions: 7 interactions with chain E Hydrophobic interactions: E:A.193, E:L.194, E:L.334, E:F.336 Hydrogen bonds: E:R.213, E:R.213 pi-Stacking: E:F.75

5 x EPE: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID(Non-functional Binders)

EPE.3: 4 residues within 4Å: Chain A: R.49, D.50, V.51, W.59 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.50, A:W.59, A:W.59 Water bridges: A:D.50 EPE.4: 5 residues within 4Å: Chain A: L.132, N.135, W.140, K.143 Chain D: V.144 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.135 Water bridges: A:W.140 Salt bridges: A:K.143 pi-Cation interactions: A:W.140, A:W.140 EPE.8: 4 residues within 4Å: Chain B: R.49, D.50, V.51, W.59 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.50, B:D.50 Water bridges: B:R.49 EPE.9: 2 residues within 4Å: Chain A: V.144 Chain B: W.140 2 PLIP interactions: 2 interactions with chain B pi-Cation interactions: B:W.140, B:W.140 EPE.23: 2 residues within 4Å: Chain B: V.144 Chain E: W.140 No protein-ligand interaction detected (PLIP)

6 x IMD: IMIDAZOLE(Non-covalent)

IMD.5: 1 residues within 4Å: Chain A: H.219 2 PLIP interactions: 2 interactions with chain A pi-Stacking: A:W.96, A:W.96 IMD.11: 1 residues within 4Å: Chain B: R.254 No protein-ligand interaction detected (PLIP) IMD.12: 3 residues within 4Å: Chain B: Q.82, W.96, H.219 2 PLIP interactions: 2 interactions with chain B pi-Stacking: B:W.96, B:W.96 IMD.18: 5 residues within 4Å: Chain D: D.65, W.66, W.322, Y.355, M.362 No protein-ligand interaction detected (PLIP) IMD.19: 1 residues within 4Å: Chain D: W.140 2 PLIP interactions: 2 interactions with chain D pi-Stacking: D:W.140, D:W.140 IMD.20: 1 residues within 4Å: Chain D: Q.82 1 PLIP interactions: 1 interactions with chain D pi-Stacking: D:W.96

2 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.10: 4 residues within 4Å: Chain B: L.52, M.236, R.243, L.251 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.243, B:R.243 TRS.17: 4 residues within 4Å: Chain D: M.236, V.239, R.243, L.251 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:R.243, D:R.243

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Brausemann, A. et al., Structure of Phytoene Desaturase Provides Insights into Herbicide Binding and Reaction Mechanisms Involved in Carotene Desaturation. Structure (2017)

Release Date

2017-07-12

Peptides

Phytoene dehydrogenase, chloroplastic/chromoplastic: ABCDE

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

Phytoene dehydrogenase, chloroplastic/chromoplastic