SMTL ID : 1o26.1

Crystal structure of Thymidylate Synthase Complementing Protein (TM0449) from Thermotoga maritima with FAD and dUMP at 1.6 A resolution

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-tetramer

Ligands

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

UMP.1: 12 residues within 4Å: Chain A: E.98, L.99, S.100, G.101, R.102, R.159 Chain D: R.86, Q.87, R.90, R.186 Ligands: FAD.10, PGE.12 16 PLIP interactions: 10 interactions with chain D, 6 interactions with chain A Hydrophobic interactions: D:Q.87, 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:Q.87, D:Q.192, A:R.159, A:R.159 Salt bridges: D:R.86, A:R.159 UMP.4: 12 residues within 4Å: Chain B: E.98, L.99, S.100, G.101, R.102, R.159 Chain C: R.86, Q.87, R.90, R.186 Ligands: PGE.6, FAD.8 17 PLIP interactions: 12 interactions with chain C, 5 interactions with chain B Hydrophobic interactions: C:Q.87, 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 Salt bridges: C:R.86, B:R.159 UMP.9: 12 residues within 4Å: Chain B: R.86, Q.87, R.90, R.186 Chain C: E.98, L.99, S.100, G.101, R.102, R.159 Ligands: FAD.5, PGE.6 17 PLIP interactions: 12 interactions with chain B, 5 interactions with chain C Hydrophobic interactions: B:Q.87, 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:R.86, B:Q.87, B:Q.192, C:R.159 Salt bridges: B:R.86, C:R.159 UMP.11: 12 residues within 4Å: Chain A: R.86, Q.87, R.90, R.186 Chain D: E.98, L.99, S.100, G.101, R.102, R.159 Ligands: FAD.2, PGE.12 18 PLIP interactions: 6 interactions with chain D, 12 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:Q.87, A:R.90

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 Chain C: 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.8, UMP.11 26 PLIP interactions: 14 interactions with chain A, 5 interactions with chain D, 7 interactions with chain C 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, A:R.186, D:A.94, D:E.98, D:E.98, C:T.67, C:N.175 Water bridges: A:R.90, D:A.94, D:Y.96, C:S.42, C:E.66, C:T.67, C:R.177 Salt bridges: A:H.91, A:H.91, A:R.92, A:R.92, C:R.177 FAD.5: 23 residues within 4Å: 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, Y.103 Chain D: S.42, T.67, E.70, I.93, N.175, R.177 Ligands: UMP.9, FAD.10, PGE.13 27 PLIP interactions: 16 interactions with chain B, 5 interactions with chain C, 6 interactions with chain D Hydrophobic interactions: B:L.185 Hydrogen bonds: B:R.90, B:R.90, B:R.92, B:I.93, B:N.181, B:N.181, B:R.186, C:S.95, C:E.98, C:E.98, D:T.67, D:N.175 Water bridges: B:R.90, B:H.91, B:H.91, B:R.92, C:A.94, C:Y.96, D:T.67, D:R.177, D:R.177 Salt bridges: B:H.91, B:H.91, B:R.92, B:R.92, D:R.177 FAD.8: 23 residues within 4Å: Chain A: S.42, T.67, E.70, I.93, N.175, R.177 Chain B: 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 Ligands: FAD.2, PGE.3, UMP.4 24 PLIP interactions: 16 interactions with chain C, 3 interactions with chain A, 5 interactions with chain B Hydrophobic interactions: C:L.185 Hydrogen bonds: C:R.90, C:R.90, C:R.92, C:R.92, C:I.93, C:N.181, C:N.181, C:R.186, A:N.175, B:A.94, B:E.98, B:E.98 Water bridges: C:R.90, C:H.91, C:H.91, A:S.42, B:A.94, B:Y.96 Salt bridges: C:H.91, C:H.91, C:R.92, C:R.92, A:R.177 FAD.10: 24 residues within 4Å: Chain A: S.95, N.97, E.98, S.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.5, PGE.7 23 PLIP interactions: 13 interactions with chain D, 6 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: D:L.185 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, A:S.100, B:N.175 Water bridges: D:R.90, A:A.94, A:Y.96, B:S.42, B:E.66 Salt bridges: D:H.91, D:H.91, D:R.92, D:R.92, B:R.177

5 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.3: 11 residues within 4Å: Chain A: A.39, S.42, G.64, H.65, E.66, T.67, P.68, R.177 Chain B: N.97 Chain C: L.185 Ligands: FAD.8 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:A.39, A:S.42, A:E.66, A:T.67 Water bridges: A:S.42 PGE.6: 9 residues within 4Å: Chain B: R.86, F.89, E.98 Chain C: A.85, R.86, F.89, E.98 Ligands: UMP.4, UMP.9 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain B Hydrogen bonds: C:R.86, C:E.98, B:R.86, B:E.98 PGE.7: 9 residues within 4Å: Chain A: N.97 Chain B: S.42, G.64, H.65, E.66, T.67, P.68, R.177 Ligands: FAD.10 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:N.97, B:S.42, B:T.67 PGE.12: 10 residues within 4Å: Chain A: A.85, R.86, F.89, E.98 Chain D: A.85, R.86, F.89, E.98 Ligands: UMP.1, UMP.11 4 PLIP interactions: 2 interactions with chain D, 2 interactions with chain A Hydrogen bonds: D:R.86, D:E.98, A:R.86, A:E.98 PGE.13: 9 residues within 4Å: Chain C: N.97 Chain D: A.39, S.42, F.43, G.64, H.65, T.67, P.68 Ligands: FAD.5 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:S.42, D:G.64 Water bridges: D:E.66, D:E.66

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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