SMTL ID : 8ren.1

Crystal structure of reduced ThyX

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.14 Å

Oligo State

homo-tetramer

Ligands

2 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.1: 6 residues within 4Å: Chain A: H.55, E.58, Y.59, K.62, H.63, Y.220 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.62 PG4.3: 6 residues within 4Å: Chain B: H.55, E.58, Y.59, K.62, H.63, Y.220 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Y.220

4 x FDA: DIHYDROFLAVINE-ADENINE DINUCLEOTIDE(Non-covalent)

FDA.2: 21 residues within 4Å: Chain A: R.90, H.91, R.92, I.93, N.181, L.185, R.186 Chain B: S.95, N.97, E.98, S.100, Y.103 Chain D: H.63, G.64, H.65, T.67, E.70, I.93, N.175, R.177 Ligands: FDA.8 23 PLIP interactions: 6 interactions with chain B, 5 interactions with chain D, 12 interactions with chain A Hydrogen bonds: B:A.94, B:N.97, B:E.98, B:E.98, B:S.100, D:H.65, D:N.175, A:R.90, A:R.90, A:R.92, A:R.92, A:I.93, A:N.181, A:N.181 Water bridges: B:S.100 Hydrophobic interactions: D:H.65, A:L.185 Salt bridges: D:R.177, A:H.91, A:H.91, A:R.92, A:R.92 pi-Stacking: D:H.65 FDA.6: 22 residues within 4Å: Chain A: A.94, S.95, N.97, E.98, S.100, Y.103 Chain B: R.90, H.91, R.92, I.93, N.181, L.185 Chain C: H.63, G.64, H.65, T.67, E.70, I.93, N.175, R.177 Ligands: PEG.5, FDA.7 25 PLIP interactions: 5 interactions with chain A, 13 interactions with chain B, 7 interactions with chain C Hydrogen bonds: A:S.95, A:N.97, A:E.98, A:E.98, A:S.100, B:R.90, B:R.90, B:R.90, B:R.92, B:R.92, B:I.93, B:N.181, B:N.181, C:H.65, C:T.67, C:N.175 Hydrophobic interactions: B:L.185, C:H.65 Salt bridges: B:H.91, B:H.91, B:R.92, B:R.92, C:R.177 Water bridges: C:N.181 pi-Stacking: C:H.65 FDA.7: 19 residues within 4Å: Chain B: H.65, T.67, E.70, I.93, N.175, R.177 Chain C: R.90, H.91, R.92, I.93, N.181, L.185 Chain D: A.94, S.95, N.97, E.98, S.100, Y.103 Ligands: FDA.6 25 PLIP interactions: 15 interactions with chain C, 6 interactions with chain B, 4 interactions with chain D Hydrophobic interactions: C:L.185, B:H.65 Hydrogen bonds: C:R.90, C:R.90, C:R.90, C:R.92, C:R.92, C:R.92, C:I.93, C:N.181, C:N.181, B:H.65, B:N.175, D:S.95, D:E.98, D:E.98, D:S.100 Water bridges: C:H.91, C:H.91, B:R.177 Salt bridges: C:H.91, C:H.91, C:R.92, B:R.177 pi-Stacking: B:H.65 FDA.8: 21 residues within 4Å: Chain A: H.63, G.64, H.65, T.67, E.70, I.93, N.175, R.177 Chain C: S.95, N.97, E.98, S.100, Y.103 Chain D: R.90, H.91, R.92, I.93, N.181, L.185, R.186 Ligands: FDA.2 24 PLIP interactions: 6 interactions with chain C, 12 interactions with chain D, 6 interactions with chain A Hydrogen bonds: C:A.94, C:N.97, C:E.98, C:E.98, C:S.100, D:R.90, D:R.90, D:R.92, D:R.92, D:I.93, D:N.181, D:N.181, A:H.65, A:T.67, A:N.175 Water bridges: C:A.94 Hydrophobic interactions: D:L.185, A:H.65 Salt bridges: D:H.91, D:H.91, D:R.92, D:R.92, A:R.177 pi-Stacking: A:H.65

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

PEG.4: 4 residues within 4Å: Chain B: S.114, E.116, R.117, W.193 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.114 PEG.5: 3 residues within 4Å: Chain B: Q.87, H.190 Ligands: FDA.6 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.87 Water bridges: B:R.90

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pecqueur, L. et al., Structural Plasticity of Flavin-Dependent Thymidylate Synthase Controlled by the Enzyme Redox State. Biomolecules (2025)

Release Date

2025-01-01

Peptides

Flavin-dependent thymidylate synthase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Flavin-dependent thymidylate synthase

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