SMTL ID : 3g4a.1

Crystal structure of flavine dependant thymidylate synthase S88A mutant from Thermotoga maritima at 1.95 angstrom resolution

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

homo-tetramer

Ligands

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

UMP.1: 12 residues within 4Å: Chain A: F.89, E.98, L.99, A.100, G.101, R.102, R.159 Chain D: R.86, Q.87, R.90, R.186 Ligands: FAD.7 15 PLIP interactions: 8 interactions with chain A, 7 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:E.98, A:R.159, A:R.159, A:R.159, D:Q.87 Salt bridges: A:R.159, D:R.86 Hydrophobic interactions: D:R.90 UMP.3: 11 residues within 4Å: Chain B: E.98, L.99, A.100, G.101, R.102, R.159 Chain C: R.86, Q.87, R.90, R.186 Ligands: FAD.5 18 PLIP interactions: 9 interactions with chain B, 9 interactions with chain C Hydrogen bonds: B:G.101, B:R.102, B:R.102, C:Q.87, C:R.90, C:R.186, C:R.186 Water bridges: B:E.98, B:E.98, B:R.159, B:R.159, B:R.159, C:Q.87, C:Q.192 Salt bridges: B:R.159, C:R.86 Hydrophobic interactions: C:Q.87, C:R.90 UMP.6: 11 residues within 4Å: Chain B: R.86, Q.87, R.90, R.186 Chain C: E.98, L.99, A.100, G.101, R.102, R.159 Ligands: FAD.4 14 PLIP interactions: 6 interactions with chain C, 8 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:Q.87 Salt bridges: C:R.159, B:R.86 Hydrophobic interactions: B:R.90 UMP.8: 12 residues within 4Å: Chain A: R.86, Q.87, R.90, R.186 Chain D: F.89, E.98, L.99, A.100, G.101, R.102, R.159 Ligands: FAD.2 17 PLIP interactions: 10 interactions with chain A, 7 interactions with chain D Hydrophobic interactions: A:R.90 Hydrogen bonds: A:Q.87, 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:Q.192, D:E.98, D:R.159, D:R.159 Salt bridges: A:R.86, D:R.159

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

FAD.2: 23 residues within 4Å: Chain A: R.90, H.91, R.92, I.93, N.181, L.185, R.186, H.190, A.191 Chain C: T.67, E.70, I.93, N.175, R.177 Chain D: A.94, S.95, N.97, E.98, A.100, R.102, Y.103 Ligands: FAD.5, UMP.8 21 PLIP interactions: 13 interactions with chain A, 4 interactions with chain C, 4 interactions with chain D 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, C:T.67, C:N.175, C:R.177, D:A.94, D:E.98, D:E.98 Water bridges: A:R.90, D:Y.96 Salt bridges: A:H.91, A:H.91, A:R.92, A:R.92, C:R.177 FAD.4: 23 residues within 4Å: Chain B: R.90, H.91, R.92, I.93, N.181, L.185, R.186, H.190, A.191 Chain C: A.94, S.95, N.97, E.98, A.100, R.102, Y.103 Chain D: T.67, E.70, I.93, N.175, R.177 Ligands: UMP.6, FAD.7 23 PLIP interactions: 15 interactions with chain B, 4 interactions with chain D, 4 interactions with chain C Hydrophobic interactions: B:L.185, B:H.190 Hydrogen bonds: B:R.90, B:R.90, B:R.92, B:I.93, B:N.181, B:N.181, D:T.67, D:N.175, D:R.177, C:S.95, C:E.98, C:E.98 Water bridges: B:R.90, B:H.91, B:H.91, C:Y.96 Salt bridges: B:H.91, B:H.91, B:R.92, B:R.92, D:R.177 FAD.5: 24 residues within 4Å: Chain A: S.42, T.67, E.70, I.93, N.175, R.177 Chain B: A.94, S.95, N.97, E.98, A.100, R.102, Y.103 Chain C: R.90, H.91, R.92, I.93, N.181, L.185, R.186, H.190, A.191 Ligands: FAD.2, UMP.3 21 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A, 16 interactions with chain C Hydrogen bonds: B:S.95, B:E.98, B:E.98, A:N.175, C:R.90, C:R.90, C:R.92, C:I.93, C:N.181, C:N.181 Salt bridges: A:R.177, C:H.91, C:H.91, C:R.92, C:R.92 Hydrophobic interactions: C:L.185, C:H.190 Water bridges: C:H.91, C:H.91, C:R.92, C:R.92 FAD.7: 23 residues within 4Å: Chain A: S.95, N.97, E.98, A.100, R.102, Y.103 Chain B: 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, A.191 Ligands: UMP.1, FAD.4 20 PLIP interactions: 4 interactions with chain A, 2 interactions with chain B, 14 interactions with chain D Hydrogen bonds: A:S.95, A:E.98, A:E.98, B:N.175, D:R.90, D:R.90, D:R.92, D:R.92, D:I.93, D:N.181, D:N.181 Water bridges: A:Y.96, D:R.90 Salt bridges: B:R.177, D:H.91, D:H.91, D:R.92, D:R.92 Hydrophobic interactions: D:L.185, D:H.190

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Koehn, E.M. et al., An unusual mechanism of thymidylate biosynthesis in organisms containing the thyX gene. Nature (2009)

Release Date

2009-04-07

Peptides

Thymidylate synthase thyX: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Thymidylate synthase thyX