SMTL ID : 4gtf.1

T. Maritima FDTS (H53A mutant) with FAD, dUMP and Folate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.77 Å

Oligo State

homo-tetramer

Ligands

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

FAD.1: 24 residues within 4Å: Chain A: A.94, S.95, N.97, E.98, S.100, R.102, Y.103 Chain C: S.42, 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, MEF.3, FAD.5 28 PLIP interactions: 19 interactions with chain D, 6 interactions with chain A, 3 interactions with chain C Hydrophobic interactions: D:L.185, D:H.190 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:N.97, 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, D:N.181, A:A.94, A:Y.96, C:R.177 Salt bridges: D:H.91, D:H.91, D:R.92, D:R.92, C:R.177 FAD.5: 24 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: S.42, T.67, E.70, I.93, N.175, R.177 Ligands: FAD.1, UMP.6, MEF.7 27 PLIP interactions: 6 interactions with chain B, 17 interactions with chain C, 4 interactions with chain D Hydrogen bonds: B:S.95, B:N.97, B:E.98, B:E.98, C:R.90, C:R.90, C:R.92, C:R.92, C:I.93, C:N.181, C:N.181, D:T.67, D:N.175 Water bridges: B:A.94, B:Y.96, C:R.90, C:R.92, C:R.92, C:N.181, D:R.177 Hydrophobic interactions: C:L.185, C:H.190 Salt bridges: C:H.91, C:H.91, C:R.92, C:R.92, D:R.177 FAD.9: 24 residues within 4Å: Chain A: S.42, 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, MEF.11, FAD.13 28 PLIP interactions: 19 interactions with chain B, 6 interactions with chain C, 3 interactions with chain A Hydrophobic interactions: B:L.185, B:H.190 Hydrogen bonds: B:R.90, B:R.90, B:R.92, B:R.92, B:I.93, B:N.181, B:N.181, C:S.95, C:N.97, C:E.98, C:E.98, A:N.175 Water bridges: B:R.90, B:H.91, B:H.91, B:R.92, B:R.92, B:N.181, C:A.94, C:Y.96, A:R.177 Salt bridges: B:H.91, B:H.91, B:R.92, B:R.92, A:R.177 FAD.13: 24 residues within 4Å: Chain A: R.90, H.91, R.92, I.93, N.181, L.185, R.186, H.190 Chain B: S.42, 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, MEF.15 27 PLIP interactions: 17 interactions with chain A, 4 interactions with chain B, 6 interactions with chain D Hydrophobic interactions: A:L.185, A:H.190 Hydrogen bonds: 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, D:S.95, D:N.97, D:E.98, D:E.98 Water bridges: A:R.90, A:R.92, A:R.92, A:N.181, B:R.177, D:A.94, D:Y.96 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 17 PLIP interactions: 6 interactions with chain A, 11 interactions with chain D Hydrogen bonds: A:G.101, A:R.102, A:R.102, D:Q.87, D:R.90, D:R.186, D:R.186 Water bridges: A:R.159, A:R.159, D:R.86, D:R.86, D:R.86, D:Q.87, D:Q.192 Salt bridges: A:R.159, D:R.86 Hydrophobic interactions: D:R.90 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 17 PLIP interactions: 6 interactions with chain C, 11 interactions with chain B Hydrogen bonds: 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: 6 interactions with chain D, 11 interactions with chain A Hydrogen bonds: 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, A:R.86, A:R.86, A:R.86, A:Q.87, A:Q.192 Salt bridges: D:R.159, A:R.86 Hydrophobic interactions: A:R.90

4 x MEF: N-({4-[(6aR)-3-amino-1-oxo-1,2,5,6,6a,7-hexahydroimidazo[1,5-f]pteridin-8(9H)-yl]phenyl}carbonyl)-L-glutamic acid(Non-covalent)

MEF.3: 12 residues within 4Å: Chain A: N.97, Y.103 Chain C: A.39, R.40, S.42, F.43, L.56, L.60, A.65, T.67 Chain D: L.185 Ligands: FAD.1 9 PLIP interactions: 7 interactions with chain C, 2 interactions with chain A Hydrophobic interactions: C:F.43, C:F.43, C:L.56 Hydrogen bonds: C:T.67, A:N.97, A:Y.103 Water bridges: C:R.40, C:R.40, C:E.66 MEF.7: 12 residues within 4Å: Chain B: N.97, Y.103 Chain C: L.185 Chain D: A.39, R.40, S.42, F.43, L.56, L.60, A.65, T.67 Ligands: FAD.5 8 PLIP interactions: 7 interactions with chain D, 1 interactions with chain B Hydrophobic interactions: D:F.43, D:F.43, D:L.56 Hydrogen bonds: D:T.67, B:N.97 Water bridges: D:R.40, D:R.40, D:E.66 MEF.11: 12 residues within 4Å: Chain A: A.39, R.40, S.42, F.43, L.56, L.60, A.65, T.67 Chain B: L.185 Chain C: N.97, Y.103 Ligands: FAD.9 9 PLIP interactions: 7 interactions with chain A, 2 interactions with chain C Hydrophobic interactions: A:F.43, A:F.43, A:L.56 Hydrogen bonds: A:T.67, C:N.97, C:Y.103 Water bridges: A:R.40, A:R.40, A:E.66 MEF.15: 12 residues within 4Å: Chain A: L.185 Chain B: A.39, R.40, S.42, F.43, L.56, L.60, A.65, T.67 Chain D: N.97, Y.103 Ligands: FAD.13 8 PLIP interactions: 7 interactions with chain B, 1 interactions with chain D Hydrophobic interactions: B:F.43, B:F.43, B:L.56 Hydrogen bonds: B:T.67, D:N.97 Water bridges: B:R.40, B:R.40, B:E.66

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

CL.4: 3 residues within 4Å: Chain A: S.107, Y.108, Y.142 Ligand excluded by PLIP CL.8: 3 residues within 4Å: Chain B: S.107, Y.108, Y.142 Ligand excluded by PLIP CL.12: 3 residues within 4Å: Chain C: S.107, Y.108, Y.142 Ligand excluded by PLIP CL.16: 3 residues within 4Å: Chain D: S.107, Y.108, Y.142 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