SMTL ID : 1o28.1

Crystal structure of Thymidylate Synthase Complementing Protein (TM0449) from Thermotoga maritima with FdUMP at 2.1 A resolution

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 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: EPE.9 16 PLIP interactions: 8 interactions with chain A, 8 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:R.86, D:R.86, D:Q.87 Salt bridges: A:R.159 Hydrophobic interactions: D:R.90 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: EPE.6 19 PLIP interactions: 11 interactions with chain C, 8 interactions with chain B Hydrophobic interactions: C:R.90 Hydrogen bonds: C:Q.87, C:R.90, C:R.186, C:R.186, B:E.98, B:G.101, B:R.102, B:R.102 Water bridges: C:R.86, C:R.86, C:Q.87, C:R.90, C:Q.192, B:R.159, B:R.159, B:R.159 Salt bridges: C:R.86, B:R.159 UFP.7: 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: EPE.4 20 PLIP interactions: 10 interactions with chain B, 10 interactions with chain C Hydrophobic interactions: B:R.90 Hydrogen bonds: B:R.86, B:Q.87, B:R.90, B:R.186, B:R.186, C:E.98, C:G.101, C:R.102, C:R.102 Water bridges: B:R.86, B:R.86, B:Q.87, B:R.90, C:E.98, C:R.159, C:R.159, C:R.159, C:R.159 Salt bridges: C:R.159 UFP.10: 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: EPE.2 17 PLIP interactions: 8 interactions with chain A, 9 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:Q.87, D:E.98, D:R.159, D:R.159, D:R.159, D:R.159 Salt bridges: D:R.159

4 x EPE: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID(Non-functional Binders)

EPE.2: 8 residues within 4Å: Chain A: R.90, H.91, R.92, N.181, L.185 Chain C: R.177 Ligands: UFP.10, PGE.12 9 PLIP interactions: 6 interactions with chain A, 2 interactions with chain C, 1 interactions with chain D Hydrogen bonds: A:R.90, A:R.92, A:N.181 Water bridges: A:R.90, A:I.93, C:T.67, D:N.97 Salt bridges: A:R.92, C:R.177 EPE.4: 6 residues within 4Å: Chain B: R.90, H.91, R.92, N.181 Chain D: R.177 Ligands: UFP.7 10 PLIP interactions: 7 interactions with chain B, 3 interactions with chain D Hydrogen bonds: B:R.90, B:R.92, B:N.181 Water bridges: B:R.90, B:R.90, B:I.93, D:R.177, D:R.177 Salt bridges: B:R.92, D:R.177 EPE.6: 9 residues within 4Å: Chain A: H.65, T.67, R.177 Chain C: R.90, H.91, R.92, N.181, R.186 Ligands: UFP.3 10 PLIP interactions: 6 interactions with chain C, 4 interactions with chain A Hydrogen bonds: C:R.90, C:R.92, C:N.181, A:H.65 Water bridges: C:I.93, A:R.177, A:R.177 Salt bridges: C:R.92, A:R.177 pi-Cation interactions: C:H.91 EPE.9: 7 residues within 4Å: Chain B: R.177 Chain D: R.90, H.91, R.92, N.181, L.185 Ligands: UFP.1 8 PLIP interactions: 1 interactions with chain B, 7 interactions with chain D Salt bridges: B:R.177, D:H.91, D:R.92 Hydrogen bonds: D:R.90, D:R.92, D:N.181 Water bridges: D:R.90, D:I.93

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

PGE.5: 9 residues within 4Å: Chain A: R.92, I.93, A.94 Chain B: E.70, I.93, N.175, R.177 Chain D: R.92, I.93 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.175, B:N.175 PGE.8: 7 residues within 4Å: Chain A: I.93, R.177, S.178 Chain B: R.92, A.94 Chain C: R.92, I.93 1 PLIP interactions: 1 interactions with chain A Water bridges: A:N.175 PGE.11: 10 residues within 4Å: Chain B: R.92, I.93 Chain C: R.92, I.93, A.94, S.95 Chain D: E.70, I.93, N.175, R.177 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:S.95, D:N.175, D:R.177 Water bridges: C:S.95 PGE.12: 8 residues within 4Å: Chain A: R.92, I.93 Chain C: E.70, I.93, R.177 Chain D: A.94, S.95 Ligands: EPE.2 6 PLIP interactions: 4 interactions with chain C, 1 interactions with chain A, 1 interactions with chain D Hydrogen bonds: C:E.70, C:R.177, A:R.92, D:S.95 Water bridges: C:N.175, C:N.175

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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