SMTL ID : 1o2b.1

Crystal structure of Thymidylate Synthase Complementing Protein (TM0449) from Thermotoga maritima with FAD and PO4 at 2.45 A resolution

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.45 Å

Oligo State

homo-tetramer

Ligands

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

PO4.1: 6 residues within 4Å: Chain A: L.99, S.100, G.101, R.102, R.159 Chain D: Q.87 9 PLIP interactions: 7 interactions with chain A, 2 interactions with chain D Hydrogen bonds: A:S.100, A:G.101, A:R.102, D:Q.87 Water bridges: A:E.98, A:R.102, A:R.159, D:R.86 Salt bridges: A:R.159 PO4.3: 6 residues within 4Å: Chain B: S.100, G.101, R.102, R.159 Chain C: R.86, Q.87 7 PLIP interactions: 5 interactions with chain B, 2 interactions with chain C Hydrogen bonds: B:G.101, B:R.102, C:Q.87 Water bridges: B:R.159, B:R.159 Salt bridges: B:R.159, C:R.86 PO4.6: 3 residues within 4Å: Chain A: R.86, Q.87 Chain D: R.159 6 PLIP interactions: 3 interactions with chain D, 3 interactions with chain A Water bridges: D:R.159, D:R.159, A:R.86 Salt bridges: D:R.159 Hydrogen bonds: A:R.86, A:Q.87

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

FAD.2: 16 residues within 4Å: Chain A: R.90, H.91, R.92, I.93, N.181, L.185, R.186 Chain C: T.67, E.70, I.93, N.175, R.177 Chain D: N.97, E.98, S.100 Ligands: FAD.5 20 PLIP interactions: 5 interactions with chain D, 12 interactions with chain A, 3 interactions with chain C Hydrogen bonds: D:S.95, D:E.98, D:E.98, D:S.100, A:R.90, A:R.90, A:R.92, A:R.92, A:R.92, A:I.93, A:N.181, A:N.181, C:T.67, C:N.175 Water bridges: D:Y.96 Hydrophobic interactions: A:L.185 Salt bridges: A:H.91, A:H.91, A:R.92, C:R.177 FAD.4: 19 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: S.95, N.97, E.98, S.100 Chain D: T.67, E.70, I.93, N.175, R.177 Ligands: FAD.7 24 PLIP interactions: 6 interactions with chain D, 14 interactions with chain B, 4 interactions with chain C Hydrogen bonds: D:T.67, D:N.175, D:R.177, B:R.90, B:R.90, B:R.92, B:R.92, B:I.93, B:N.181, B:N.181, B:R.186, C:S.95, C:E.98, C:E.98 Water bridges: D:R.177, B:H.91, C:R.102 Salt bridges: D:R.177, B:H.91, B:H.91, B:R.92, B:R.92 pi-Cation interactions: D:H.65 Hydrophobic interactions: B:L.185 FAD.5: 20 residues within 4Å: Chain A: S.42, T.67, E.70, I.93, N.175, R.177, S.178 Chain B: 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 Ligands: FAD.2 23 PLIP interactions: 4 interactions with chain A, 15 interactions with chain C, 4 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, C:R.186, B:S.95, B:E.98, B:E.98 Water bridges: A:S.42, C:H.91, C:H.91, B:R.102 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 FAD.7: 19 residues within 4Å: Chain A: S.95, N.97, E.98, S.100 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 Ligands: FAD.4 22 PLIP interactions: 14 interactions with chain D, 4 interactions with chain B, 4 interactions with chain A 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, D:R.186, B:N.175, A:S.95, A:E.98, A:E.98 Salt bridges: D:H.91, D:H.91, D:R.92, D:R.92, B:R.177 Water bridges: B:R.177, A:R.102 pi-Cation interactions: B:H.65

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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