SMTL ID : 5ios.1

Flavin-dependent thymidylate synthase R90A variant in complex with FAD and deoxyuridine monophosphate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-tetramer

Ligands

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

FAD.1: 20 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 Chain C: T.67, E.70, I.93, N.175, R.177 Ligands: UMP.2, FAD.5 23 PLIP interactions: 15 interactions with chain A, 3 interactions with chain C, 5 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, A:R.186, C:N.175, B:S.95, B:E.98, B:E.98, B:S.100 Water bridges: A:H.91, A:H.91, C:T.67, B:Y.96 Salt bridges: A:H.91, A:H.91, A:R.92, A:R.92, C:R.177 FAD.4: 22 residues within 4Å: Chain A: S.95, N.97, E.98, S.100, Y.103 Chain B: R.90, H.91, R.92, I.93, N.181, L.185, R.186, H.190, A.191 Chain D: S.42, T.67, E.70, I.93, N.175, R.177 Ligands: UMP.3, FAD.7 23 PLIP interactions: 4 interactions with chain D, 14 interactions with chain B, 5 interactions with chain A Hydrogen bonds: D:T.67, D:N.175, B:R.90, B:R.90, B:R.92, B:R.92, B:I.93, B:N.181, B:N.181, A:S.95, A:E.98, A:E.98 Water bridges: D:T.67, B:H.91, B:H.91, A:A.94, A:Y.96 Salt bridges: D:R.177, B:H.91, B:H.91, B:R.92, B:R.92 Hydrophobic interactions: B:L.185 FAD.5: 22 residues within 4Å: Chain A: 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 Chain D: A.94, S.95, N.97, E.98, S.100, Y.103 Ligands: FAD.1, UMP.8 22 PLIP interactions: 14 interactions with chain C, 3 interactions with chain A, 5 interactions with chain D Hydrophobic interactions: C:L.185 Hydrogen bonds: C:R.90, C:R.90, C:R.92, C:R.92, C:I.93, C:N.181, C:N.181, C:R.186, A:T.67, A:N.175, D:A.94, D:E.98, D:E.98 Water bridges: C:R.90, D:A.94, D:Y.96 Salt bridges: C:H.91, C:H.91, C:R.92, C:R.92, A:R.177 FAD.7: 20 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 Chain D: R.90, H.91, R.92, I.93, N.181, L.185, R.186, H.190 Ligands: FAD.4, UMP.6 21 PLIP interactions: 3 interactions with chain B, 5 interactions with chain C, 13 interactions with chain D Hydrogen bonds: B:N.175, C:S.95, 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, D:R.186 Water bridges: B:T.67, C:Y.96 Salt bridges: B:R.177, D:H.91, D:H.91, D:R.92, D:R.92 Hydrophobic interactions: D:L.185

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

UMP.2: 9 residues within 4Å: Chain A: R.86, Q.87, R.90, R.186 Chain B: E.98, L.99, S.100, R.159 Ligands: FAD.1 17 PLIP interactions: 8 interactions with chain B, 9 interactions with chain A Hydrogen bonds: B:E.98, B:S.100, A:Q.87, A:R.90, A:R.186, A:R.186 Water bridges: B:E.98, B:E.98, B:R.155, B:R.155, B:R.159, A:R.86, A:Q.87, A:Q.192 Salt bridges: B:R.159, A:R.86 Hydrophobic interactions: A:R.90 UMP.3: 12 residues within 4Å: Chain A: F.89, E.98, L.99, S.100, G.101, A.102, R.159 Chain B: R.86, Q.87, R.90, R.186 Ligands: FAD.4 13 PLIP interactions: 8 interactions with chain B, 5 interactions with chain A Hydrophobic interactions: B:Q.87, B:R.90 Hydrogen bonds: B:Q.87, B:R.90, B:R.186, B:R.186, A:G.101, A:A.102 Water bridges: B:Q.87, B:Q.192, A:R.159, A:R.159 Salt bridges: A:R.159 UMP.6: 9 residues within 4Å: Chain C: E.98, L.99, S.100, R.159 Chain D: R.86, Q.87, R.90, R.186 Ligands: FAD.7 13 PLIP interactions: 9 interactions with chain D, 4 interactions with chain C Hydrophobic interactions: D:R.90 Hydrogen bonds: D:Q.87, D:R.90, D:R.186, D:R.186 Water bridges: D:R.86, D:Q.87, D:Q.192, C:E.98, C:E.98, C:R.159 Salt bridges: D:R.86, C:R.159 UMP.8: 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, A.102, R.159 Ligands: FAD.5 12 PLIP interactions: 7 interactions with chain C, 5 interactions with chain D Hydrophobic interactions: C:R.90 Hydrogen bonds: C:Q.87, C:R.90, C:R.186, C:R.186, D:G.101, D:A.102 Water bridges: C:Q.87, C:Q.192, D:R.159, D:R.159 Salt bridges: D:R.159

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