SMTL ID : 5ioq.1

Flavin-dependent thymidylate synthase in complex with FAD and deoxyuridine

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.93 Å

Oligo State

homo-tetramer

Ligands

4 x FAD: FLAVIN-ADENINE DINUCLEOTIDE(Non-covalent)

FAD.1: 22 residues within 4Å: Chain A: R.90, H.91, R.92, I.93, N.181, L.185, R.186, H.190 Chain B: A.94, S.95, N.97, E.98, S.100, R.102 Chain C: T.67, E.70, I.93, N.175, R.177 Ligands: DUR.9, FAD.12, PGE.14 22 PLIP interactions: 16 interactions with chain A, 3 interactions with chain C, 3 interactions with chain B 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, C:N.175, B:S.95, B:E.98, B:E.98 Water bridges: A:H.91, A:H.91, A:R.92, A:R.92, C:E.66 Salt bridges: A:H.91, A:H.91, A:R.92, A:R.92, C:R.177 FAD.7: 21 residues within 4Å: Chain A: 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 Chain D: T.67, E.70, I.93, N.175, R.177 Ligands: PGE.3, DUR.8, FAD.17 29 PLIP interactions: 17 interactions with chain B, 8 interactions with chain A, 4 interactions with chain D Hydrophobic interactions: B:L.185 Hydrogen bonds: B:R.90, B:R.90, B:R.92, B:R.92, B:I.93, B:N.181, B:N.181, A:A.94, A:E.98, A:E.98, D:T.67, D:N.175 Water bridges: B:R.90, B:H.91, B:H.91, B:R.92, B:R.92, A:A.94, A:Y.96, A:Y.96, A:S.100, A:S.100, D:T.67 Salt bridges: B:H.91, B:H.91, B:R.92, B:R.92, D:R.177 FAD.12: 21 residues within 4Å: Chain A: 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 Chain D: S.95, N.97, E.98, S.100, R.102 Ligands: FAD.1, PGE.5, DUR.13 21 PLIP interactions: 3 interactions with chain A, 6 interactions with chain D, 12 interactions with chain C Hydrogen bonds: A:T.67, A:N.175, D:A.94, D:E.98, D:E.98, C:R.90, C:R.90, C:R.92, C:R.92, C:I.93, C:N.181, C:N.181 Salt bridges: A:R.177, C:H.91, C:H.91, C:R.92, C:R.92 Water bridges: D:A.94, D:S.100, D:S.100 Hydrophobic interactions: C:L.185 FAD.17: 23 residues within 4Å: Chain B: T.67, E.70, I.93, N.175, R.177 Chain C: A.94, S.95, N.97, E.98, S.100, R.102 Chain D: R.90, H.91, R.92, I.93, N.181, L.185, R.186, H.190, A.191 Ligands: FAD.7, PGE.11, DUR.18 23 PLIP interactions: 3 interactions with chain B, 5 interactions with chain C, 15 interactions with chain D Hydrogen bonds: B:N.175, C:S.95, C:E.98, C:E.98, D:R.90, D:R.90, D:R.92, D:R.92, D:I.93, D:N.181, D:N.181 Water bridges: B:T.67, C:Y.96, C:Y.96, D:R.90, D:R.92, D:R.92 Salt bridges: B:R.177, D:H.91, D:H.91, D:R.92, D:R.92 Hydrophobic interactions: D:L.185

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

PGE.2: 7 residues within 4Å: Chain A: L.99, G.101, E.156, R.159, T.168 Chain B: L.164 Ligands: DUR.8 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.98, A:T.168 PGE.3: 5 residues within 4Å: Chain A: N.97 Chain D: L.60, H.65, T.67 Ligands: FAD.7 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:G.64 Water bridges: D:E.66 PGE.4: 6 residues within 4Å: Chain A: H.55, E.58, Y.59, K.62, H.63, Y.220 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.58, A:E.58, A:K.62 PGE.5: 9 residues within 4Å: Chain A: A.39, L.60, G.64, H.65, T.67, P.68 Chain C: L.185 Chain D: N.97 Ligands: FAD.12 2 PLIP interactions: 2 interactions with chain A Water bridges: A:E.66, A:E.66 PGE.6: 13 residues within 4Å: Chain A: R.86, Q.87, L.164, Q.192 Chain B: E.98, L.99, G.101, R.102, L.106, E.156, R.159, T.168 Ligands: DUR.9 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:R.86, A:R.86, A:Q.87, A:Q.192, B:E.98 PGE.10: 5 residues within 4Å: Chain B: H.55, E.58, Y.59, K.62, Y.220 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:E.58, B:E.58, B:K.62, B:Y.220 PGE.11: 8 residues within 4Å: Chain B: L.60, G.64, H.65, T.67, P.68 Chain C: N.97 Chain D: L.185 Ligands: FAD.17 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:H.65, B:R.177 Water bridges: B:E.66, B:T.67 PGE.14: 6 residues within 4Å: Chain A: L.185 Chain C: G.64, H.65, E.66, R.177 Ligands: FAD.1 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:E.66 PGE.15: 13 residues within 4Å: Chain C: E.98, L.99, G.101, R.102, L.106, E.156, R.159, T.168 Chain D: R.86, Q.87, L.164, Q.192 Ligands: DUR.18 6 PLIP interactions: 3 interactions with chain D, 3 interactions with chain C Hydrogen bonds: D:R.86, D:Q.87, D:Q.192, C:E.98, C:E.98, C:T.168 PGE.16: 12 residues within 4Å: Chain C: R.86, Q.87, L.164, Q.192 Chain D: E.98, L.99, G.101, R.102, E.156, R.159, T.168 Ligands: DUR.13 7 PLIP interactions: 4 interactions with chain C, 3 interactions with chain D Hydrogen bonds: C:R.86, C:R.86, C:Q.87, C:Q.192, D:E.98, D:E.98 Water bridges: D:G.101

4 x DUR: 2'-DEOXYURIDINE(Non-covalent)

DUR.8: 12 residues within 4Å: Chain A: F.89, E.98, L.99, S.100, G.101, R.102 Chain B: R.86, Q.87, R.90, R.186 Ligands: PGE.2, FAD.7 8 PLIP interactions: 6 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:R.90 Hydrogen bonds: B:R.90, B:R.186, B:R.186, A:G.101, A:R.102 Water bridges: B:R.86, B:Q.87 DUR.9: 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 Ligands: FAD.1, PGE.6 8 PLIP interactions: 6 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:R.90 Hydrogen bonds: A:R.90, A:R.186, A:R.186, B:G.101, B:R.102 Water bridges: A:R.86, A:Q.87 DUR.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 Ligands: FAD.12, PGE.16 9 PLIP interactions: 2 interactions with chain D, 7 interactions with chain C Hydrogen bonds: D:G.101, D:R.102, C:R.90, C:R.186, C:R.186 Hydrophobic interactions: C:R.90 Water bridges: C:R.86, C:Q.87, C:Q.192 DUR.18: 12 residues within 4Å: Chain C: F.89, E.98, L.99, S.100, G.101, R.102 Chain D: R.86, Q.87, R.90, R.186 Ligands: PGE.15, FAD.17 8 PLIP interactions: 2 interactions with chain C, 6 interactions with chain D Hydrogen bonds: C:G.101, C:R.102, D:R.90, D:R.186, D:R.186 Hydrophobic interactions: D:R.90 Water bridges: D:R.86, D:Q.87

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Stull, F.W. et al., Deprotonations in the Reaction of Flavin-Dependent Thymidylate Synthase. Biochemistry (2016)

Release Date

2016-06-08

Peptides

Thymidylate synthase ThyX: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Thymidylate synthase ThyX

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