SMTL ID : 1o29.1

Crystal structure of Thymidylate Synthase Complementing Protein (TM0449) from Thermotoga maritima with FAD and FdUMP at 2.0 A resolution

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-tetramer

Ligands

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

UFP.1: 13 residues within 4Å: Chain A: F.89, E.98, L.99, S.100, G.101, R.102, Y.103, R.159 Chain D: R.86, Q.87, R.90, R.186 Ligands: FAD.7 17 PLIP interactions: 10 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: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, A:R.159 Salt bridges: A:R.159 UFP.3: 13 residues within 4Å: Chain B: F.89, E.98, L.99, S.100, G.101, R.102, Y.103, R.159 Chain C: R.86, Q.87, R.90, R.186 Ligands: FAD.5 15 PLIP interactions: 7 interactions with chain B, 8 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:R.159, B:R.159, B:R.159, C:R.86, C:R.86, C:Q.87 Salt bridges: B:R.159 Hydrophobic interactions: C:R.90 UFP.6: 13 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, Y.103, R.159 Ligands: FAD.4 17 PLIP interactions: 8 interactions with chain B, 9 interactions with chain C Hydrophobic interactions: B:R.90 Hydrogen bonds: B:Q.87, B:R.90, B:R.186, B:R.186, C:G.101, C:R.102, C:R.102 Water bridges: B:R.86, B:R.86, B:Q.87, C:R.159, C:R.159, C:R.159, C:R.159 Salt bridges: C:R.159 Halogen bonds: C:S.100 UFP.8: 13 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, Y.103, R.159 Ligands: FAD.2 18 PLIP interactions: 10 interactions with chain A, 8 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, D:R.159 Salt bridges: D:R.159 Halogen bonds: D:S.100

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

FAD.2: 20 residues within 4Å: Chain A: R.90, H.91, R.92, I.93, N.181, L.185, R.186, H.190 Chain C: T.67, E.70, I.93, N.175, R.177 Chain D: S.95, N.97, E.98, S.100, Y.103 Ligands: FAD.5, UFP.8 26 PLIP interactions: 16 interactions with chain A, 4 interactions with chain C, 6 interactions with chain D Hydrophobic interactions: A:L.185, A:H.190, 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, C:T.67, C:N.175, D:S.95, D:E.98, D:E.98 Water bridges: A:R.90, A:R.92, A:R.92, C:T.67, D:A.94, D: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 B: R.90, H.91, R.92, I.93, N.181, L.185, R.186, H.190 Chain C: S.95, N.97, E.98, S.100, Y.103 Chain D: S.42, H.65, T.67, E.70, I.93, N.175, R.177 Ligands: UFP.6, FAD.7 29 PLIP interactions: 5 interactions with chain C, 6 interactions with chain D, 18 interactions with chain B Hydrogen bonds: C:A.94, C:E.98, C:E.98, 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 Water bridges: C:A.94, C:Y.96, D:E.66, D:T.67, B:R.90, B:H.91, B:H.91, B:R.92, B:R.92 Salt bridges: D:R.177, B:H.91, B:H.91, B:R.92, B:R.92 pi-Stacking: D:H.65 Hydrophobic interactions: B:L.185, B:H.190 FAD.5: 23 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, S.100, 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, UFP.3 32 PLIP interactions: 8 interactions with chain A, 18 interactions with chain C, 6 interactions with chain B Hydrogen bonds: A:N.175, C:R.90, C:R.90, C:R.92, C:R.92, C:I.93, C:N.181, C:N.181, B:A.94, B:E.98, B:E.98 Water bridges: A:H.65, A:T.67, A:T.67, A:R.177, A:R.177, C:R.90, C:H.91, C:H.91, C:R.92, C:R.92, B:A.94, B:Y.96, B:Y.96 Salt bridges: A:R.177, C:H.91, C:H.91, C:R.92, C:R.92 pi-Cation interactions: A:H.65 Hydrophobic interactions: C:L.185, C:H.190 FAD.7: 23 residues within 4Å: Chain A: A.94, S.95, N.97, E.98, S.100, 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: UFP.1, FAD.4 25 PLIP interactions: 16 interactions with chain D, 4 interactions with chain A, 5 interactions with chain B 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:E.98, A:E.98, B:N.175 Water bridges: D:R.90, D:R.92, D:R.92, A:Y.96, B:S.42, B:R.177, B:R.177 Salt bridges: D:H.91, D:H.91, D:R.92, D:R.92, B:R.177

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mathews, I.I. et al., Functional Analysis of Substrate and Cofactor Complex Structures of a Thymidylate Synthase-Complementing Protein. Structure (2003)

Release Date

2003-06-24

Peptides

Thymidylate synthase thyX: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Thymidylate synthase thyX

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