SMTL ID : 1o27.1

Crystal structure of Thymidylate Synthase Complementing Protein (TM0449) from Thermotoga maritima with FAD and BrdUMP at 2.3 A resolution

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-tetramer

Ligands

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

BRU.1: 12 residues within 4Å: Chain A: 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 14 PLIP interactions: 6 interactions with chain A, 8 interactions with chain D Hydrogen bonds: A:G.101, A:R.102, A:R.102, D:R.86, D:Q.87, D:R.90, D:R.186, D:R.186 Water bridges: A:R.159, A:R.159, D:Q.87 Salt bridges: A:R.159 Hydrophobic interactions: D:Q.87, D:R.90 BRU.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 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 BRU.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 16 PLIP interactions: 6 interactions with chain C, 10 interactions with chain B Hydrogen bonds: C:G.101, C:R.102, C:R.102, B:R.86, 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:Q.87, B:R.90 BRU.8: 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, Y.103, R.159 Ligands: FAD.2 16 PLIP interactions: 8 interactions with chain D, 8 interactions with chain A Hydrogen bonds: D:G.101, D:R.102, D:R.102, A:Q.87, A:Q.87, A:R.90, A:R.186, A:R.186 Water bridges: D:R.159, D:R.159, D:R.159, D:R.159, A:Q.192 Salt bridges: D:R.159 Hydrophobic interactions: A:Q.87, A:R.90

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

FAD.2: 22 residues within 4Å: Chain A: R.90, H.91, R.92, I.93, N.181, L.185, R.186, H.190 Chain C: H.65, T.67, E.70, I.93, N.175, R.177, S.178 Chain D: S.95, N.97, E.98, S.100, Y.103 Ligands: FAD.5, BRU.8 23 PLIP interactions: 5 interactions with chain D, 3 interactions with chain C, 15 interactions with chain A Hydrogen bonds: D:A.94, D:E.98, D:E.98, C:T.67, C:N.175, A:R.90, A:R.90, A:R.92, A:R.92, A:I.93, A:N.181, A:N.181, A:R.186 Water bridges: D:A.94, D:Y.96, A:R.90 Salt bridges: C:R.177, A:H.91, A:H.91, A:R.92, A:R.92 Hydrophobic interactions: A:L.185, A:H.190 FAD.4: 21 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 Chain D: S.42, T.67, E.70, I.93, N.175, R.177 Ligands: BRU.6, FAD.7 25 PLIP interactions: 5 interactions with chain D, 16 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:I.93, B:N.181, B:N.181, B:R.186, C:S.95, C:E.98, C:E.98 Water bridges: D:E.66, B:R.90, B:H.91, B:H.91, C:Y.96 Salt bridges: D:R.177, B:H.91, B:H.91, B:R.92, B:R.92 Hydrophobic interactions: B:L.185, B:H.190 FAD.5: 23 residues within 4Å: Chain A: S.42, H.65, 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 Ligands: FAD.2, BRU.3 26 PLIP interactions: 17 interactions with chain C, 3 interactions with chain B, 6 interactions with chain A Hydrophobic interactions: C:L.185, C:H.190 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, B:E.98, B:E.98, A:S.42, A:N.175, A:N.175 Water bridges: C:R.90, C:H.91, C:H.91, B:Y.96, A:H.65, A:T.67 Salt bridges: C:H.91, C:H.91, C:R.92, C:R.92, A:R.177 FAD.7: 22 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 Ligands: BRU.1, FAD.4 22 PLIP interactions: 5 interactions with chain A, 14 interactions with chain D, 3 interactions with chain B Hydrogen bonds: A:S.95, A:E.98, A:E.98, D:R.90, D:R.90, D:R.92, D:R.92, D:I.93, D:N.181, D:N.181, B:N.175, B:R.177 Water bridges: A:A.94, A:Y.96, D:R.90 Hydrophobic interactions: D:L.185, D:H.190 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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