SMTL ID : 1jh7.2 (2 other biounits)

Semi-reduced Inhibitor-bound Cyclic Nucleotide Phosphodiesterase from Arabidopsis thaliana

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-hexamer

Ligands

24 x SO4: SULFATE ION(Non-functional Binders)

SO4.1: 1 residues within 4Å: Chain A: S.78 Ligand excluded by PLIP SO4.2: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP SO4.3: 5 residues within 4Å: Ligands: SO4.4, SO4.9, SO4.10, SO4.15, SO4.16 Ligand excluded by PLIP SO4.4: 8 residues within 4Å: Chain A: E.28 Chain B: E.28 Chain C: E.28 Ligands: SO4.3, SO4.9, SO4.10, SO4.15, SO4.16 Ligand excluded by PLIP SO4.7: 1 residues within 4Å: Chain B: S.78 Ligand excluded by PLIP SO4.8: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP SO4.9: 5 residues within 4Å: Ligands: SO4.3, SO4.4, SO4.10, SO4.15, SO4.16 Ligand excluded by PLIP SO4.10: 8 residues within 4Å: Chain A: E.28 Chain B: E.28 Chain C: E.28 Ligands: SO4.3, SO4.4, SO4.9, SO4.15, SO4.16 Ligand excluded by PLIP SO4.13: 1 residues within 4Å: Chain C: S.78 Ligand excluded by PLIP SO4.14: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP SO4.15: 5 residues within 4Å: Ligands: SO4.3, SO4.4, SO4.9, SO4.10, SO4.16 Ligand excluded by PLIP SO4.16: 8 residues within 4Å: Chain A: E.28 Chain B: E.28 Chain C: E.28 Ligands: SO4.3, SO4.4, SO4.9, SO4.10, SO4.15 Ligand excluded by PLIP SO4.19: 1 residues within 4Å: Chain D: S.78 Ligand excluded by PLIP SO4.20: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP SO4.21: 5 residues within 4Å: Ligands: SO4.22, SO4.27, SO4.28, SO4.33, SO4.34 Ligand excluded by PLIP SO4.22: 8 residues within 4Å: Chain D: E.28 Chain E: E.28 Chain F: E.28 Ligands: SO4.21, SO4.27, SO4.28, SO4.33, SO4.34 Ligand excluded by PLIP SO4.25: 1 residues within 4Å: Chain E: S.78 Ligand excluded by PLIP SO4.26: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP SO4.27: 5 residues within 4Å: Ligands: SO4.21, SO4.22, SO4.28, SO4.33, SO4.34 Ligand excluded by PLIP SO4.28: 8 residues within 4Å: Chain D: E.28 Chain E: E.28 Chain F: E.28 Ligands: SO4.21, SO4.22, SO4.27, SO4.33, SO4.34 Ligand excluded by PLIP SO4.31: 1 residues within 4Å: Chain F: S.78 Ligand excluded by PLIP SO4.32: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP SO4.33: 5 residues within 4Å: Ligands: SO4.21, SO4.22, SO4.27, SO4.28, SO4.34 Ligand excluded by PLIP SO4.34: 8 residues within 4Å: Chain D: E.28 Chain E: E.28 Chain F: E.28 Ligands: SO4.21, SO4.22, SO4.27, SO4.28, SO4.33 Ligand excluded by PLIP

12 x UVC: URIDINE-2',3'-VANADATE(Non-covalent)

UVC.5: 12 residues within 4Å: Chain A: S.10, W.12, H.42, T.44, F.84, H.119, S.121, Y.124, T.161, T.163, W.171 Chain F: Y.50 9 PLIP interactions: 8 interactions with chain A, 1 interactions with chain F Hydrogen bonds: A:S.10, A:T.44, A:T.44, A:S.121, A:Y.124, A:T.161, A:T.161, A:T.163, F:Y.50 UVC.6: 10 residues within 4Å: Chain A: R.31, G.36, P.37, R.38, F.39, L.168 Chain B: R.31 Chain C: R.31 Ligands: UVC.12, UVC.18 7 PLIP interactions: 4 interactions with chain A, 1 interactions with chain C, 2 interactions with chain B Hydrophobic interactions: A:P.37 Hydrogen bonds: A:G.36, A:P.37, A:R.38, C:R.31, B:R.31, B:R.31 UVC.11: 12 residues within 4Å: Chain B: S.10, W.12, H.42, T.44, F.84, H.119, S.121, Y.124, T.161, T.163, W.171 Chain E: Y.50 9 PLIP interactions: 8 interactions with chain B, 1 interactions with chain E Hydrogen bonds: B:S.10, B:T.44, B:T.44, B:S.121, B:Y.124, B:T.161, B:T.161, B:T.163, E:Y.50 UVC.12: 10 residues within 4Å: Chain A: R.31 Chain B: R.31, G.36, P.37, R.38, F.39, L.168 Chain C: R.31 Ligands: UVC.6, UVC.18 7 PLIP interactions: 4 interactions with chain B, 2 interactions with chain C, 1 interactions with chain A Hydrophobic interactions: B:P.37 Hydrogen bonds: B:G.36, B:P.37, B:R.38, C:R.31, C:R.31, A:R.31 UVC.17: 12 residues within 4Å: Chain C: S.10, W.12, H.42, T.44, F.84, H.119, S.121, Y.124, T.161, T.163, W.171 Chain D: Y.50 9 PLIP interactions: 8 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:S.10, C:T.44, C:T.44, C:S.121, C:Y.124, C:T.161, C:T.161, C:T.163, D:Y.50 UVC.18: 10 residues within 4Å: Chain A: R.31 Chain B: R.31 Chain C: R.31, G.36, P.37, R.38, F.39, L.168 Ligands: UVC.6, UVC.12 7 PLIP interactions: 4 interactions with chain C, 2 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: C:P.37 Hydrogen bonds: C:G.36, C:P.37, C:R.38, A:R.31, A:R.31, B:R.31 UVC.23: 12 residues within 4Å: Chain C: Y.50 Chain D: S.10, W.12, H.42, T.44, F.84, H.119, S.121, Y.124, T.161, T.163, W.171 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:S.10, D:T.44, D:T.44, D:S.121, D:T.161, D:T.163 UVC.24: 10 residues within 4Å: Chain D: R.31, G.36, P.37, R.38, F.39, L.168 Chain E: R.31 Chain F: R.31 Ligands: UVC.30, UVC.36 7 PLIP interactions: 4 interactions with chain D, 2 interactions with chain E, 1 interactions with chain F Hydrophobic interactions: D:P.37 Hydrogen bonds: D:G.36, D:P.37, D:R.38, E:R.31, E:R.31, F:R.31 UVC.29: 12 residues within 4Å: Chain B: Y.50 Chain E: S.10, W.12, H.42, T.44, F.84, H.119, S.121, Y.124, T.161, T.163, W.171 6 PLIP interactions: 6 interactions with chain E Hydrogen bonds: E:S.10, E:T.44, E:T.44, E:S.121, E:T.161, E:T.163 UVC.30: 10 residues within 4Å: Chain D: R.31 Chain E: R.31, G.36, P.37, R.38, F.39, L.168 Chain F: R.31 Ligands: UVC.24, UVC.36 7 PLIP interactions: 2 interactions with chain F, 4 interactions with chain E, 1 interactions with chain D Hydrogen bonds: F:R.31, F:R.31, E:G.36, E:P.37, E:R.38, D:R.31 Hydrophobic interactions: E:P.37 UVC.35: 12 residues within 4Å: Chain A: Y.50 Chain F: S.10, W.12, H.42, T.44, F.84, H.119, S.121, Y.124, T.161, T.163, W.171 6 PLIP interactions: 6 interactions with chain F Hydrogen bonds: F:S.10, F:T.44, F:T.44, F:S.121, F:T.161, F:T.163 UVC.36: 10 residues within 4Å: Chain D: R.31 Chain E: R.31 Chain F: R.31, G.36, P.37, R.38, F.39, L.168 Ligands: UVC.24, UVC.30 7 PLIP interactions: 1 interactions with chain E, 4 interactions with chain F, 2 interactions with chain D Hydrogen bonds: E:R.31, F:G.36, F:P.37, F:R.38, D:R.31, D:R.31 Hydrophobic interactions: F:P.37

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hofmann, A. et al., Crystal structures of the semireduced and inhibitor-bound forms of cyclic nucleotide phosphodiesterase from Arabidopsis thaliana. J.Biol.Chem. (2002)

Release Date

2002-02-06

Peptides

cyclic phosphodiesterase: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

E
A

F
A

cyclic phosphodiesterase

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