SMTL ID : 4gtb.1

T. Maritima FDTS with FAD, dUMP, and Raltitrexed.

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-tetramer

Ligands

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

FAD.1: 23 residues within 4Å: Chain A: A.94, 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: UMP.2, D16.3, FAD.5 27 PLIP interactions: 18 interactions with chain D, 4 interactions with chain C, 5 interactions with chain A Hydrophobic interactions: D:L.185, A:Y.103 Hydrogen bonds: D:R.90, D:R.90, D:R.92, D:R.92, D:I.93, D:N.181, D:N.181, C:N.175, C:N.175, A:E.98, A:E.98 Water bridges: D:R.90, D:H.91, D:H.91, D:R.92, D:R.92, D:N.181, C:R.177, A:A.94, A:Y.96 Salt bridges: D:H.91, D:H.91, D:R.92, D:R.92, C:R.177 FAD.5: 23 residues within 4Å: Chain B: A.94, 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: FAD.1, UMP.6, D16.7 26 PLIP interactions: 16 interactions with chain C, 5 interactions with chain B, 5 interactions with chain D Hydrophobic interactions: C:L.185, B:Y.103 Hydrogen bonds: C:R.90, C:R.90, C:R.92, C:R.92, C:I.93, C:N.181, C:N.181, B:E.98, B:E.98, D:T.67, D:N.175, D:N.175 Water bridges: C:R.90, C:R.92, C:R.92, C:N.181, B:A.94, B:Y.96, D:R.177 Salt bridges: C:H.91, C:H.91, C:R.92, C:R.92, D:R.177 FAD.9: 23 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: A.94, S.95, N.97, E.98, S.100, R.102, Y.103 Ligands: UMP.10, D16.11, FAD.13 27 PLIP interactions: 4 interactions with chain A, 18 interactions with chain B, 5 interactions with chain C Hydrogen bonds: A:N.175, A:N.175, B:R.90, B:R.90, B:R.92, B:R.92, B:I.93, B:N.181, B:N.181, C:E.98, C:E.98 Water bridges: A:R.177, B:R.90, B:H.91, B:H.91, B:R.92, B:R.92, B:N.181, C:A.94, C:Y.96 Salt bridges: A:R.177, B:H.91, B:H.91, B:R.92, B:R.92 Hydrophobic interactions: B:L.185, C:Y.103 FAD.13: 23 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: A.94, S.95, N.97, E.98, S.100, R.102, Y.103 Ligands: FAD.9, UMP.14, D16.15 26 PLIP interactions: 16 interactions with chain A, 5 interactions with chain D, 5 interactions with chain B Hydrophobic interactions: A:L.185, D:Y.103 Hydrogen bonds: A:R.90, A:R.90, A:R.92, A:R.92, A:I.93, A:N.181, A:N.181, D:E.98, D:E.98, B:T.67, B:N.175, B:N.175 Water bridges: A:R.90, A:R.92, A:R.92, A:N.181, D:A.94, D:Y.96, B:R.177 Salt bridges: A:H.91, A:H.91, A:R.92, A:R.92, B:R.177

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

UMP.2: 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.1 18 PLIP interactions: 11 interactions with chain D, 7 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:G.101, A:R.102, A:R.102 Water bridges: D:R.86, D:R.86, D:R.86, D:Q.87, D:Q.192, A:R.159, A:R.159 Salt bridges: D:R.86, A:R.159 UMP.6: 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.5 17 PLIP interactions: 11 interactions with chain C, 6 interactions with chain B Hydrophobic interactions: C:R.90 Hydrogen bonds: C:Q.87, C:R.90, C:R.186, C:R.186, B:G.101, B:R.102, B:R.102 Water bridges: C:R.86, C:R.86, C:R.86, C:Q.87, C:Q.192, B:R.159, B:R.159 Salt bridges: C:R.86, B:R.159 UMP.10: 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.9 18 PLIP interactions: 7 interactions with chain C, 11 interactions with chain B Hydrogen bonds: C:E.98, C:G.101, C:R.102, C:R.102, B:Q.87, B:R.90, B:R.186, B:R.186 Water bridges: C:R.159, C:R.159, B:R.86, B:R.86, B:R.86, B:Q.87, B:Q.192 Salt bridges: C:R.159, B:R.86 Hydrophobic interactions: B:R.90 UMP.14: 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.13 17 PLIP interactions: 11 interactions with chain A, 6 interactions with chain D Hydrophobic interactions: A:R.90 Hydrogen bonds: A:Q.87, A:R.90, A:R.186, A:R.186, D:G.101, D:R.102, D:R.102 Water bridges: A:R.86, A:R.86, A:R.86, A:Q.87, A:Q.192, D:R.159, D:R.159 Salt bridges: A:R.86, D:R.159

4 x D16: TOMUDEX(Non-covalent)

D16.3: 6 residues within 4Å: Chain C: L.60, G.64, H.65, T.67 Chain D: L.185 Ligands: FAD.1 4 PLIP interactions: 1 interactions with chain D, 3 interactions with chain C Hydrophobic interactions: D:L.185 Water bridges: C:E.66 pi-Stacking: C:H.65, C:H.65 D16.7: 6 residues within 4Å: Chain C: L.185 Chain D: L.60, G.64, H.65, T.67 Ligands: FAD.5 4 PLIP interactions: 3 interactions with chain D, 1 interactions with chain C Water bridges: D:E.66 pi-Stacking: D:H.65, D:H.65 Hydrophobic interactions: C:L.185 D16.11: 6 residues within 4Å: Chain A: L.60, G.64, H.65, T.67 Chain B: L.185 Ligands: FAD.9 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Water bridges: A:E.66 pi-Stacking: A:H.65, A:H.65 Hydrophobic interactions: B:L.185 D16.15: 6 residues within 4Å: Chain A: L.185 Chain B: L.60, G.64, H.65, T.67 Ligands: FAD.13 4 PLIP interactions: 1 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:L.185 Water bridges: B:E.66 pi-Stacking: B:H.65, B:H.65

4 x CL: CHLORIDE ION(Non-functional Binders)

CL.4: 2 residues within 4Å: Chain A: S.107, Y.108 Ligand excluded by PLIP CL.8: 2 residues within 4Å: Chain B: S.107, Y.108 Ligand excluded by PLIP CL.12: 2 residues within 4Å: Chain C: S.107, Y.108 Ligand excluded by PLIP CL.16: 2 residues within 4Å: Chain D: S.107, Y.108 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Koehn, E.M. et al., Folate binding site of flavin-dependent thymidylate synthase. Proc.Natl.Acad.Sci.USA (2012)

Release Date

2012-10-17

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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