SMTL ID : 6j61.1

Crystal Structure of Thymidylate Synthase, Thy1, from Thermus thermophilus having an Extra C Terminal Domain

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-tetramer

Ligands

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

FAD.1: 24 residues within 4Å: Chain A: H.55, R.56, H.57, S.59, E.62, T.85, D.173, H.175, N.176 Chain B: R.84, T.85, A.86, S.87, N.89, E.90, S.92 Chain D: R.82, H.83, R.84, T.85, H.179, L.183 Ligands: FAD.10, PO4.12 26 PLIP interactions: 10 interactions with chain A, 5 interactions with chain B, 11 interactions with chain D Hydrophobic interactions: A:H.55, A:H.57 Hydrogen bonds: A:H.57, A:T.58, A:S.59, A:S.59, A:H.175, A:N.176, B:R.84, B:A.86, B:E.90, B:E.90, D:R.82, D:R.84, D:T.85, D:T.85 pi-Stacking: A:H.57, A:H.57 Water bridges: B:S.92 Salt bridges: D:H.83, D:H.83, D:R.84, D:R.84, D:H.179, D:H.179 pi-Cation interactions: D:R.84 FAD.6: 23 residues within 4Å: Chain A: R.84, T.85, A.86, N.89, E.90, S.92, Y.95 Chain B: H.55, H.57, T.58, S.59, E.62, T.85, H.175, N.176 Chain C: R.82, H.83, R.84, T.85, H.179, L.183 Ligands: FAD.7, PO4.9 23 PLIP interactions: 11 interactions with chain C, 9 interactions with chain B, 3 interactions with chain A Hydrogen bonds: C:R.84, C:R.84, C:T.85, C:T.85, B:H.57, B:T.58, B:S.59, B:S.59, B:H.175, B:N.176, A:T.85, A:E.90, A:E.90 Salt bridges: C:H.83, C:H.83, C:R.84, C:R.84, C:H.179, C:H.179 pi-Cation interactions: C:R.84, B:H.57 pi-Stacking: B:H.57, B:H.57 FAD.7: 23 residues within 4Å: Chain B: R.82, H.83, R.84, T.85, H.179, L.183 Chain C: H.55, H.57, T.58, S.59, E.62, T.85, D.173, H.175, N.176 Chain D: R.84, T.85, A.86, V.88, N.89, E.90 Ligands: PO4.4, FAD.6 25 PLIP interactions: 13 interactions with chain B, 9 interactions with chain C, 3 interactions with chain D Hydrogen bonds: B:R.84, B:R.84, B:T.85, B:T.85, C:H.57, C:T.58, C:S.59, C:S.59, C:H.175, C:N.176, D:R.84, D:E.90, D:E.90 Water bridges: B:R.82, B:R.84, B:R.84 Salt bridges: B:H.83, B:H.83, B:R.84, B:R.84, B:H.179 pi-Cation interactions: B:R.84 Hydrophobic interactions: C:H.57 pi-Stacking: C:H.57, C:H.57 FAD.10: 23 residues within 4Å: Chain A: R.82, H.83, R.84, T.85, H.179, L.183 Chain C: R.84, T.85, A.86, N.89, E.90, S.92, Y.95 Chain D: H.55, H.57, T.58, S.59, E.62, D.173, H.175, N.176 Ligands: FAD.1, PO4.2 28 PLIP interactions: 6 interactions with chain C, 13 interactions with chain A, 9 interactions with chain D Hydrogen bonds: C:R.84, C:A.86, C:E.90, C:E.90, A:R.84, A:R.84, A:T.85, A:T.85, D:H.57, D:T.58, D:T.58, D:S.59, D:S.59, D:H.175, D:N.176 Water bridges: C:S.92, C:S.92, A:H.83, A:Q.172 Salt bridges: A:H.83, A:H.83, A:R.84, A:R.84, A:H.179 pi-Cation interactions: A:R.84, A:R.84 pi-Stacking: D:H.57, D:H.57

8 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.2: 6 residues within 4Å: Chain A: Q.79, R.82, R.184 Chain C: R.94 Ligands: PO4.8, FAD.10 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:Q.79, C:R.94 Salt bridges: A:R.82, A:R.184 PO4.3: 8 residues within 4Å: Chain A: S.92, G.93, R.94, R.157 Chain C: R.78, Q.79, R.82 Ligands: PO4.9 7 PLIP interactions: 5 interactions with chain C, 2 interactions with chain A Hydrogen bonds: C:Q.79, A:G.93 Water bridges: C:R.78, C:R.78 Salt bridges: C:R.78, C:R.82, A:R.157 PO4.4: 5 residues within 4Å: Chain B: Q.79, R.82, R.184 Ligands: FAD.7, PO4.11 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.79 Salt bridges: B:R.82, B:R.184 PO4.5: 8 residues within 4Å: Chain B: S.92, G.93, R.94, R.157 Chain D: R.78, Q.79, R.82 Ligands: PO4.12 8 PLIP interactions: 4 interactions with chain D, 4 interactions with chain B Hydrogen bonds: D:Q.79, B:G.93, B:R.94 Water bridges: D:R.78, B:I.91 Salt bridges: D:R.78, D:R.82, B:R.157 PO4.8: 7 residues within 4Å: Chain A: Q.79, R.82 Chain C: S.92, G.93, R.94, R.157 Ligands: PO4.2 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain C Hydrogen bonds: A:Q.79, C:G.93 Salt bridges: A:R.78, A:R.82, C:R.157 PO4.9: 6 residues within 4Å: Chain A: R.94 Chain C: Q.79, R.82, R.184 Ligands: PO4.3, FAD.6 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:Q.79 Salt bridges: C:R.82, C:R.184 PO4.11: 7 residues within 4Å: Chain B: Q.79, R.82 Chain D: S.92, G.93, R.94, R.157 Ligands: PO4.4 4 PLIP interactions: 2 interactions with chain D, 2 interactions with chain B Hydrogen bonds: D:G.93, B:Q.79 Salt bridges: D:R.157, B:R.82 PO4.12: 5 residues within 4Å: Chain D: Q.79, R.82, R.184 Ligands: FAD.1, PO4.5 2 PLIP interactions: 2 interactions with chain D Salt bridges: D:R.82, D:R.184

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ogawa, A. et al., Crystal structure of the flavin-dependent thymidylate synthase Thy1 from Thermus thermophilus with an extra C-terminal domain. Acta Crystallogr.,Sect.F (2019)

Release Date

2019-06-26

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