SMTL ID : 5ior.1

Flavin-dependent thymidylate synthase in complex with FAD and 2'-deoxyuridine-5'-monosulfate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.95 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: T.67, E.70, I.93, N.175, R.177 Chain D: S.95, N.97, E.98, S.100, R.102, Y.103 Ligands: DUS.2, RBF.3, FAD.4 27 PLIP interactions: 7 interactions with chain D, 15 interactions with chain A, 5 interactions with chain B Hydrogen bonds: D:S.95, D:E.98, D:E.98, A:R.90, A:R.90, A:R.92, A:R.92, A:I.93, A:N.181, A:N.181, B:T.67, B:N.175 Water bridges: D:A.94, D:Y.96, D:N.97, D:N.97, A:R.90, A:R.92, A:R.92, B:R.177, B:R.177 Hydrophobic interactions: A:L.185 Salt bridges: A:H.91, A:H.91, A:R.92, A:R.92, B:R.177 FAD.4: 22 residues within 4Å: Chain A: T.67, E.70, I.93, N.175, R.177 Chain B: R.90, H.91, R.92, I.93, N.181, L.185, R.186, H.190 Chain C: S.95, N.97, E.98, S.100, R.102, Y.103 Ligands: FAD.1, DUS.5, RBF.6 28 PLIP interactions: 7 interactions with chain C, 17 interactions with chain B, 4 interactions with chain A Hydrogen bonds: C:S.95, C:E.98, C:E.98, B:R.90, B:R.90, B:R.92, B:R.92, B:I.93, B:N.181, B:N.181, A:N.175 Water bridges: C:A.94, C:Y.96, C:N.97, C:N.97, B:R.90, B:H.91, B:H.91, B:R.92, B:R.92, A:R.177, A:R.177 Hydrophobic interactions: B:L.185 Salt bridges: B:H.91, B:H.91, B:R.92, B:R.92, A:R.177 FAD.7: 22 residues within 4Å: Chain B: S.95, N.97, E.98, S.100, R.102, Y.103 Chain C: 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: DUS.8, RBF.9, FAD.10 27 PLIP interactions: 5 interactions with chain D, 15 interactions with chain C, 7 interactions with chain B Hydrogen bonds: D:T.67, D:N.175, C:R.90, C:R.90, C:R.92, C:R.92, C:I.93, C:N.181, C:N.181, B:S.95, B:E.98, B:E.98 Water bridges: D:R.177, D:R.177, C:R.90, C:R.92, C:R.92, B:A.94, B:Y.96, B:N.97, B:N.97 Salt bridges: D:R.177, C:H.91, C:H.91, C:R.92, C:R.92 Hydrophobic interactions: C:L.185 FAD.10: 22 residues within 4Å: Chain A: S.95, N.97, E.98, S.100, R.102, Y.103 Chain C: T.67, E.70, I.93, N.175, R.177 Chain D: R.90, H.91, R.92, I.93, N.181, L.185, R.186, H.190 Ligands: FAD.7, DUS.11, RBF.12 28 PLIP interactions: 17 interactions with chain D, 7 interactions with chain A, 4 interactions with chain C 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, A:S.95, A:E.98, A:E.98, C:N.175 Water bridges: D:R.90, D:H.91, D:H.91, D:R.92, D:R.92, A:A.94, A:Y.96, A:N.97, A:N.97, C:R.177, C:R.177 Salt bridges: D:H.91, D:H.91, D:R.92, D:R.92, C:R.177

4 x DUS: 2'-deoxy-5'-O-sulfouridine(Non-covalent)

DUS.2: 12 residues within 4Å: Chain A: 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: FAD.1 17 PLIP interactions: 8 interactions with chain D, 9 interactions with chain A Hydrogen bonds: D:E.98, D:G.101, D:R.102, D:R.102, A:Q.87, A:R.90, A:R.186, A:R.186 Water bridges: D:R.159, D:R.159, D:R.159, A:R.86, A:Q.87, A:Q.192 Salt bridges: D:R.159, A:R.86 Hydrophobic interactions: A:R.90 DUS.5: 12 residues within 4Å: Chain B: R.86, Q.87, R.90, R.186 Chain C: F.89, E.98, L.99, S.100, G.101, R.102, R.159 Ligands: FAD.4 18 PLIP interactions: 9 interactions with chain B, 9 interactions with chain C Hydrophobic interactions: B:R.90 Hydrogen bonds: B:Q.87, B:R.90, B:R.186, B:R.186, C:E.98, C:E.98, C:G.101, C:R.102, C:R.102 Water bridges: B:R.86, B:Q.87, B:Q.192, C:R.159, C:R.159, C:R.159 Salt bridges: B:R.86, C:R.159 DUS.8: 12 residues within 4Å: Chain B: F.89, E.98, L.99, S.100, G.101, R.102, R.159 Chain C: R.86, Q.87, R.90, R.186 Ligands: FAD.7 17 PLIP interactions: 9 interactions with chain C, 8 interactions with chain B Hydrophobic interactions: C:R.90 Hydrogen bonds: C:Q.87, C:R.90, C:R.186, C:R.186, B:E.98, B:G.101, B:R.102, B:R.102 Water bridges: C:R.86, C:Q.87, C:Q.192, B:R.159, B:R.159, B:R.159 Salt bridges: C:R.86, B:R.159 DUS.11: 12 residues within 4Å: Chain A: 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: FAD.10 18 PLIP interactions: 9 interactions with chain D, 9 interactions with chain A Hydrophobic interactions: D:R.90 Hydrogen bonds: D:Q.87, D:R.90, D:R.186, D:R.186, A:E.98, A:E.98, A:G.101, A:R.102, A:R.102 Water bridges: D:R.86, D:Q.87, D:Q.192, A:R.159, A:R.159, A:R.159 Salt bridges: D:R.86, A:R.159

4 x RBF: RIBOFLAVIN(Non-covalent)

RBF.3: 8 residues within 4Å: Chain B: A.39, L.56, Y.59, H.65, T.67 Chain D: N.97, Y.103 Ligands: FAD.1 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain D Hydrophobic interactions: B:H.65 Hydrogen bonds: B:Y.59 Water bridges: D:R.102, D:Y.103 pi-Stacking: D:Y.103 RBF.6: 8 residues within 4Å: Chain A: A.39, L.56, Y.59, H.65, T.67 Chain C: N.97, Y.103 Ligands: FAD.4 6 PLIP interactions: 2 interactions with chain A, 4 interactions with chain C Hydrophobic interactions: A:H.65 Hydrogen bonds: A:Y.59, C:Y.103 Water bridges: C:R.102, C:Y.103 pi-Stacking: C:Y.103 RBF.9: 8 residues within 4Å: Chain B: N.97, Y.103 Chain D: A.39, L.56, Y.59, H.65, T.67 Ligands: FAD.7 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain D Water bridges: B:R.102, B:Y.103 pi-Stacking: B:Y.103 Hydrophobic interactions: D:H.65 Hydrogen bonds: D:Y.59 RBF.12: 8 residues within 4Å: Chain A: N.97, Y.103 Chain C: A.39, L.56, Y.59, H.65, T.67 Ligands: FAD.10 6 PLIP interactions: 2 interactions with chain C, 4 interactions with chain A Hydrophobic interactions: C:H.65 Hydrogen bonds: C:Y.59, A:Y.103 Water bridges: A:R.102, A:Y.103 pi-Stacking: A:Y.103

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
A

C
A

D
A

Thymidylate synthase ThyX

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