SMTL ID : 6khp.1

Crystal structure of Oryza sativa TDC with PLP and tryptamine

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-tetramer

Ligands

4 x PLP: PYRIDOXAL-5'-PHOSPHATE(Covalent)

PLP.1: 13 residues within 4Å: Chain A: F.104, T.174, T.175, S.176, H.214, T.269, G.271, D.298, A.300, Y.301, K.330 Chain B: V.380, G.381 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:T.269, A:A.300, A:K.330 Hydrogen bonds: A:T.175, A:T.175, A:S.176 Water bridges: A:H.214, A:K.330 Salt bridges: A:K.330 pi-Stacking: A:H.214 PLP.8: 14 residues within 4Å: Chain A: G.379, V.380, G.381 Chain B: F.104, T.174, T.175, S.176, H.214, G.271, T.273, D.298, A.300, K.330 Ligands: TSS.2 9 PLIP interactions: 2 interactions with chain A, 7 interactions with chain B Hydrogen bonds: A:V.380, A:G.381, B:T.175, B:S.176, B:K.330 Hydrophobic interactions: B:K.330 Water bridges: B:H.214 Salt bridges: B:K.330 pi-Stacking: B:H.214 PLP.12: 13 residues within 4Å: Chain C: F.104, T.174, T.175, S.176, H.214, T.269, G.271, D.298, A.300, Y.301, K.330 Chain D: V.380, G.381 10 PLIP interactions: 10 interactions with chain C Hydrophobic interactions: C:T.269, C:A.300, C:K.330 Hydrogen bonds: C:T.175, C:S.176 Water bridges: C:H.214, C:K.330, C:K.330 Salt bridges: C:K.330 pi-Stacking: C:H.214 PLP.19: 14 residues within 4Å: Chain C: G.379, V.380, G.381 Chain D: F.104, T.174, T.175, S.176, H.214, G.271, T.273, D.298, A.300, K.330 Ligands: TSS.13 11 PLIP interactions: 2 interactions with chain C, 9 interactions with chain D Hydrogen bonds: C:V.380, C:G.381, D:T.175, D:T.175, D:S.176 Hydrophobic interactions: D:K.330 Water bridges: D:H.214, D:T.339, D:T.339 Salt bridges: D:K.330 pi-Stacking: D:H.214

2 x TSS: 2-(1H-INDOL-3-YL)ETHANAMINE(Covalent)

TSS.2: 10 residues within 4Å: Chain A: V.125, F.127, Y.359, G.381 Chain B: W.95, F.104, H.214, H.329, K.330 Ligands: PLP.8 6 PLIP interactions: 3 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:V.125, A:F.127, B:W.95, B:K.330 Hydrogen bonds: A:G.381 pi-Cation interactions: B:K.330 TSS.13: 10 residues within 4Å: Chain C: V.125, F.127, Y.359, G.381 Chain D: W.95, F.104, H.214, H.329, K.330 Ligands: PLP.19 6 PLIP interactions: 3 interactions with chain C, 3 interactions with chain D Hydrophobic interactions: C:V.125, C:F.127, D:W.95, D:K.330 Hydrogen bonds: C:G.381 pi-Cation interactions: D:K.330

8 x CA: CALCIUM ION(Non-covalent)

CA.3: 1 residues within 4Å: Chain A: D.408 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:D.408, H2O.1, H2O.2, H2O.4, H2O.6 CA.4: 1 residues within 4Å: Chain A: S.365 No protein-ligand interaction detected (PLIP) CA.9: 1 residues within 4Å: Chain B: D.408 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:D.408, H2O.9, H2O.10, H2O.11, H2O.12 CA.10: 1 residues within 4Å: Chain A: D.64 No protein-ligand interaction detected (PLIP) CA.14: 1 residues within 4Å: Chain C: D.408 5 PLIP interactions: 1 interactions with chain C, 4 Ligand-Water interactions Metal complexes: C:D.408, H2O.17, H2O.18, H2O.20, H2O.22 CA.15: 1 residues within 4Å: Chain C: S.365 No protein-ligand interaction detected (PLIP) CA.20: 1 residues within 4Å: Chain D: D.408 5 PLIP interactions: 1 interactions with chain D, 4 Ligand-Water interactions Metal complexes: D:D.408, H2O.24, H2O.26, H2O.26, H2O.28 CA.21: 1 residues within 4Å: Chain C: D.64 No protein-ligand interaction detected (PLIP)

4 x ACT: ACETATE ION(Non-functional Binders)

ACT.5: 4 residues within 4Å: Chain A: P.357, Y.359 Chain B: H.214, S.215 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:Y.359 Water bridges: A:E.358, A:Y.359 Hydrogen bonds: B:S.215 Salt bridges: B:H.214 ACT.6: 6 residues within 4Å: Chain A: Q.23, P.24, L.25, N.26 Chain B: S.491, L.492 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:S.491, A:L.25 Hydrophobic interactions: A:Q.23 ACT.16: 4 residues within 4Å: Chain C: P.357, Y.359 Chain D: H.214, S.215 5 PLIP interactions: 3 interactions with chain C, 2 interactions with chain D Hydrophobic interactions: C:Y.359 Water bridges: C:E.358, C:Y.359 Hydrogen bonds: D:S.215 Salt bridges: D:H.214 ACT.17: 6 residues within 4Å: Chain C: Q.23, P.24, L.25, N.26 Chain D: S.491, L.492 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain D Hydrophobic interactions: C:Q.23 Hydrogen bonds: C:L.25, D:S.491

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

PEG.7: 9 residues within 4Å: Chain A: V.140, L.143, D.144, F.156, M.157, N.158, G.168, G.169, Y.342 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:F.156, A:N.158, A:G.169 PEG.11: 2 residues within 4Å: Chain B: E.310, R.406 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.406 PEG.18: 9 residues within 4Å: Chain C: V.140, L.143, D.144, F.156, M.157, N.158, G.168, G.169, Y.342 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:F.156, C:N.158, C:G.169 PEG.22: 2 residues within 4Å: Chain D: E.310, R.406 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:R.406 Water bridges: D:E.310

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhou, Y. et al., Crystal structure ofOryza sativaTDC reveals the substrate specificity for TDC-mediated melatonin biosynthesis. J Adv Res (2020)

Release Date

2020-07-15

Peptides

Tryptophan decarboxylase 1: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Tryptophan decarboxylase 1

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