SMTL ID : 8reo.1

Crystal structure of reduced ThyX in complex with dUMP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.03 Å

Oligo State

homo-tetramer

Ligands

4 x UMP: 2'-DEOXYURIDINE 5'-MONOPHOSPHATE(Non-covalent)

UMP.1: 12 residues within 4Å: Chain A: F.89, E.98, L.99, S.100, G.101, R.102, R.159 Chain B: R.86, Q.87, R.90, R.186 Ligands: FDA.8 15 PLIP interactions: 8 interactions with chain B, 7 interactions with chain A Hydrophobic interactions: B:R.90 Hydrogen bonds: B:Q.87, B:R.90, B:R.186, B:R.186, A:S.100, A:G.101, A:R.102, A:R.102 Water bridges: B:Q.87, B:Q.192, A:R.159, A:R.159 Salt bridges: B:R.86, A:R.159 UMP.5: 12 residues within 4Å: Chain A: R.86, Q.87, R.90, R.186 Chain B: F.89, E.98, L.99, S.100, G.101, R.102, R.159 Ligands: FDA.3 16 PLIP interactions: 9 interactions with chain B, 7 interactions with chain A Hydrogen bonds: B:S.100, B:G.101, B:R.102, B:R.102, A:Q.87, A:R.90, A:R.186, A:R.186 Water bridges: B:R.159, B:R.159, B:R.159, B:R.159, A:Q.87, A:Q.192 Salt bridges: B:R.159 Hydrophobic interactions: A:R.90 UMP.9: 12 residues within 4Å: Chain C: F.89, E.98, L.99, S.100, G.101, R.102, R.159 Chain D: R.86, Q.87, R.90, R.186 Ligands: FDA.15 17 PLIP interactions: 10 interactions with chain D, 7 interactions with chain C Hydrophobic interactions: D:R.90 Hydrogen bonds: D:Q.87, D:R.90, D:R.186, D:R.186, C:G.101, C:R.102, C:R.102 Water bridges: D:R.86, D:R.86, D:R.86, D:Q.87, D:Q.192, C:R.159, C:R.159, C:R.159 Salt bridges: C:R.159 UMP.13: 12 residues within 4Å: Chain C: R.86, Q.87, R.90, R.186 Chain D: F.89, E.98, L.99, S.100, G.101, R.102, R.159 Ligands: FDA.11 17 PLIP interactions: 7 interactions with chain D, 10 interactions with chain C Hydrogen bonds: D:S.100, D:G.101, D:R.102, D:R.102, C:Q.87, C:R.90, C:R.186, C:R.186 Water bridges: D:R.159, D:R.159, C:R.86, C:Q.87, C:Q.192 Salt bridges: D:R.159, C:R.86 Hydrophobic interactions: C:Q.87, C:R.90

1 x P6G: HEXAETHYLENE GLYCOL(Non-functional Binders)

P6G.2: 9 residues within 4Å: Chain A: A.39, S.42, F.43, Y.59, G.64, H.65, T.67 Chain C: Y.103 Ligands: FDA.15 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.42

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

FDA.3: 24 residues within 4Å: Chain A: R.90, H.91, R.92, I.93, N.181, L.185, R.186, H.190, A.191 Chain B: A.94, S.95, N.97, E.98, S.100, R.102 Chain D: S.42, T.67, E.70, I.93, N.175, R.177 Ligands: UMP.5, PG4.14, FDA.15 21 PLIP interactions: 14 interactions with chain A, 4 interactions with chain B, 3 interactions with chain D Hydrophobic interactions: A:L.185 Hydrogen bonds: A:R.90, A:R.90, A:R.92, A:R.92, A:I.93, A:N.181, A:N.181, A:R.186, B:S.95, B:E.98, B:E.98, D:N.175, D:R.177 Water bridges: A:R.90, B:Y.96 Salt bridges: A:H.91, A:H.91, A:R.92, A:R.92, D:R.177 FDA.8: 23 residues within 4Å: Chain A: A.94, S.95, N.97, E.98, S.100, R.102 Chain B: R.90, H.91, R.92, I.93, N.181, L.185, R.186, H.190, A.191 Chain C: T.67, E.70, I.93, N.175, R.177 Ligands: UMP.1, FDA.11, PEG.12 20 PLIP interactions: 3 interactions with chain C, 13 interactions with chain B, 4 interactions with chain A Hydrogen bonds: C:T.67, C:N.175, B:R.90, B:R.90, B:R.92, B:R.92, B:I.93, B:N.181, B:N.181, B:R.186, A:S.95, A:E.98, A:E.98 Salt bridges: C:R.177, B:H.91, B:H.91, B:R.92, B:R.92 Hydrophobic interactions: B:L.185 Water bridges: A:A.94 FDA.11: 23 residues within 4Å: Chain B: S.42, T.67, E.70, I.93, N.175, R.177 Chain C: R.90, H.91, R.92, I.93, N.181, L.185, R.186, H.190, A.191 Chain D: A.94, S.95, N.97, E.98, S.100 Ligands: PEG.6, FDA.8, UMP.13 23 PLIP interactions: 3 interactions with chain B, 16 interactions with chain C, 4 interactions with chain D Hydrogen bonds: B:N.175, C:R.90, C:R.90, C:R.92, C:R.92, C:I.93, C:N.181, C:N.181, C:R.186, D:S.95, D:E.98, D:E.98 Water bridges: B:E.66, C:R.90, C:H.91, C:H.91, D:Y.96 Salt bridges: B:R.177, C:H.91, C:H.91, C:R.92, C:R.92 Hydrophobic interactions: C:L.185 FDA.15: 23 residues within 4Å: Chain A: S.42, T.67, E.70, I.93, N.175, R.177 Chain C: A.94, S.95, N.97, E.98, S.100 Chain D: R.90, H.91, R.92, I.93, N.181, L.185, R.186, H.190, A.191 Ligands: P6G.2, FDA.3, UMP.9 23 PLIP interactions: 16 interactions with chain D, 4 interactions with chain C, 3 interactions with chain A Hydrophobic interactions: D:L.185 Hydrogen bonds: D:R.90, D:R.90, D:R.92, D:R.92, D:I.93, D:N.181, D:N.181, D:R.186, C:S.95, C:E.98, C:E.98, A:T.67, A:N.175 Water bridges: D:R.90, D:H.91, D:H.91, C:Y.96 Salt bridges: D:H.91, D:H.91, D:R.92, D:R.92, A:R.177

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

PG4.4: 6 residues within 4Å: Chain B: H.55, E.58, Y.59, K.62, H.63, Y.220 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.58, B:K.62, B:Y.220 PG4.14: 9 residues within 4Å: Chain B: Y.103 Chain D: S.42, F.43, L.60, G.64, H.65, T.67, P.68 Ligands: FDA.3 4 PLIP interactions: 2 interactions with chain D, 2 interactions with chain B Hydrogen bonds: D:S.42, D:H.65, B:Y.103, B:Y.103

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

PEG.6: 6 residues within 4Å: Chain B: G.64, H.65, E.66, T.67 Chain C: L.185 Ligands: FDA.11 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain D Hydrogen bonds: B:E.66, D:N.97 Water bridges: B:S.42 PEG.10: 3 residues within 4Å: Chain C: Y.108, S.135, D.139 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:D.139 PEG.12: 3 residues within 4Å: Chain C: H.65, T.67 Ligands: FDA.8 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:H.65 Water bridges: C:A.39, A:N.97

1 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.7: 5 residues within 4Å: Chain B: S.114, E.116, R.117, E.119, W.193 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.114

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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