SMTL ID : 6kho.1

Crystal structure of Oryza sativa TDC with PLP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.97 Å

Oligo State

homo-dimer

Ligands

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

PLP.1: 13 residues within 4Å: Chain A: F.104, T.174, T.175, S.176, H.214, G.271, T.273, D.298, A.300, Y.301, K.330 Chain B: V.380, G.381 13 PLIP interactions: 2 interactions with chain B, 11 interactions with chain A Hydrogen bonds: B:V.380, B:G.381, A:T.175, A:T.175, A:S.176, A:T.216, A:T.216 Hydrophobic interactions: A:K.330 Water bridges: A:T.175, A:H.214, A:H.329, A:H.329 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: ACT.2 9 PLIP interactions: 6 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:A.300, B:K.330 Hydrogen bonds: B:T.175, B:S.176, B:K.330, A:V.380, A:G.381 Water bridges: B:H.214, A:G.381

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

ACT.2: 6 residues within 4Å: Chain A: F.127, Y.359 Chain B: F.104, K.330 Ligands: PLP.8, ACT.9 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Salt bridges: B:K.330 Hydrogen bonds: A:Y.359 ACT.3: 7 residues within 4Å: Chain A: W.95, F.104, P.105, S.106, H.329, K.330 Chain B: V.125 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Water bridges: A:K.330, A:K.330 Salt bridges: A:K.330 Hydrophobic interactions: B:V.125 ACT.9: 8 residues within 4Å: Chain A: V.125 Chain B: W.95, F.104, S.106, H.329, K.330, L.336 Ligands: ACT.2 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:K.330, B:L.336, A:V.125 Salt bridges: B:K.330 ACT.10: 5 residues within 4Å: Chain A: P.357, Y.359 Chain B: H.214, S.215, T.273 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:S.215 Salt bridges: B:H.214 Hydrophobic interactions: A:Y.359 Water bridges: A:E.358, A:Y.359

4 x CA: CALCIUM ION(Non-covalent)(Non-functional Binders)

CA.4: 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.1, H2O.2, H2O.9 CA.5: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) CA.11: 1 residues within 4Å: Chain B: D.408 6 PLIP interactions: 1 interactions with chain B, 5 Ligand-Water interactions Metal complexes: B:D.408, H2O.11, H2O.11, H2O.13, H2O.17, H2O.19 CA.12: 1 residues within 4Å: Chain A: D.64 No protein-ligand interaction detected (PLIP)

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

PEG.6: 6 residues within 4Å: Chain A: P.71, T.72, Y.73, S.74, A.75 Chain B: R.394 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:T.72, A:Y.73, B:R.394, B:R.394 PEG.7: 6 residues within 4Å: Chain A: Q.130, K.361, N.362, H.363 Chain B: F.103, Y.472 7 PLIP interactions: 2 interactions with chain B, 5 interactions with chain A Water bridges: B:N.466, B:N.466, A:N.362, A:A.364 Hydrogen bonds: A:K.361, A:H.363, A:H.363

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: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Tryptophan decarboxylase 1

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