SMTL ID : 4kas.1

Crystal structure of FDTS from T. maritima mutant (H53D) with FAD and dUMP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

homo-tetramer

Ligands

3 x DU: 2'-DEOXYURIDINE-5'-MONOPHOSPHATE(Non-covalent)

DU.1: 12 residues within 4Å: Chain A: F.89, E.98, L.99, S.100, G.101, R.102, R.159 Chain D: R.86, Q.87, R.90, R.186 Ligands: FAD.8 45 PLIP interactions: 9 interactions with chain A, 8 interactions with chain D, 16 interactions with chain B, 12 interactions with chain C Hydrogen bonds: A:E.98, A:G.101, A:R.102, A:R.102, D:Q.87, D:R.90, D:R.186, D:R.186, B:Q.87, B:R.90, B:E.98, B:E.98, B:G.101, B:R.102, B:R.102, B:R.186, B:R.186, C:Q.87, C:R.90, C:E.98, C:E.98, C:R.186, C:R.186 Water bridges: A:R.159, A:R.159, A:R.159, A:R.159, D:R.86, D:Q.87, B:Q.87, B:R.159, B:R.159, B:R.159, C:Q.87, C:E.98, C:R.159, C:R.159 Salt bridges: A:R.159, B:R.159, C:R.159 Hydrophobic interactions: D:Q.87, D:R.90, B:Q.87, B:R.90, C:R.90 DU.3: 12 residues within 4Å: Chain B: F.89, E.98, L.99, S.100, G.101, R.102, R.159 Chain C: R.86, Q.87, R.90, R.186 Ligands: FAD.5 Protein-ligand interaction information (PLIP) not available DU.6: 7 residues within 4Å: Chain B: R.86, Q.87, R.90, R.186 Chain C: F.89, E.98, R.159 Protein-ligand interaction information (PLIP) not available

2 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 5 residues within 4Å: Chain A: R.90, H.91, R.92, I.93, N.181 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:R.92, A:I.93, A:N.181 Salt bridges: A:H.91, A:R.92 Water bridges: C:R.177 SO4.4: 5 residues within 4Å: Chain B: R.90, H.91, R.92, I.93, N.181 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:R.90, B:H.91, B:R.92, B:I.93, B:N.181 Salt bridges: B:R.92

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

FAD.5: 22 residues within 4Å: Chain A: S.42, D.65, T.67, E.70, I.93, N.175, R.177, S.178 Chain B: 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: DU.3 21 PLIP interactions: 15 interactions with chain C, 3 interactions with chain B, 3 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, B:S.95, B:E.98, B:E.98, A:N.175, A:R.177 Water bridges: C:H.91, C:H.91 Salt bridges: C:H.91, C:H.91, C:R.92, C:R.92, A:R.177 FAD.8: 23 residues within 4Å: Chain A: S.95, N.97, E.98, S.100, Y.103 Chain B: S.42, D.65, T.67, E.70, I.93, N.175, R.177, S.178 Chain D: R.90, H.91, R.92, I.93, S.178, N.181, L.185, R.186, H.190 Ligands: DU.1 18 PLIP interactions: 10 interactions with chain D, 5 interactions with chain B, 3 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, B:S.42, B:N.175, B:R.177, B:R.177, A:S.95, A:E.98, A:E.98 Salt bridges: D:R.92, D:R.92, B:R.177

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.7: 2 residues within 4Å: Chain C: Y.220, Y.222 Ligand excluded by PLIP

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

PO4.9: 2 residues within 4Å: Chain A: Q.87 Chain D: R.159 8 PLIP interactions: 6 interactions with chain D, 2 interactions with chain A Water bridges: D:L.99, D:R.155, D:R.155, D:R.159, D:R.159, A:R.86 Salt bridges: D:R.159 Hydrogen bonds: A:Q.87

1 x 2PE: NONAETHYLENE GLYCOL(Non-covalent)

2PE.10: 5 residues within 4Å: Chain D: H.55, E.58, Y.59, K.62, Y.220 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:K.62, D:Y.220

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mathews, I.I., Flavin-Dependent Thymidylate Synthase as a Drug Target for Deadly Microbes: Mutational Study and a Strategy for Inhibitor Design. J Bioterror Biodef (2013)

Release Date

2014-03-26

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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