SMTL ID : 6r2e.2 (3 other biounits)

Crystal structure of the human thymidylate synthase (hTS) interface variant Q62R

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.55 Å

Oligo State

homo-dimer

Ligands

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

SO4.1: 8 residues within 4Å: Chain A: R.187, R.188 Chain B: R.62, L.204, P.205, C.207, R.227, S.228 7 PLIP interactions: 4 interactions with chain A, 3 interactions with chain B Water bridges: A:R.187, A:R.187 Salt bridges: A:R.187, A:R.188, B:R.62, B:R.227 Hydrogen bonds: B:S.228 SO4.2: 8 residues within 4Å: Chain A: R.62, L.204, P.205, C.207, R.227, S.228 Chain B: R.187, R.188 6 PLIP interactions: 3 interactions with chain B, 3 interactions with chain A Water bridges: B:R.187 Salt bridges: B:R.187, B:R.188, A:R.62, A:R.227 Hydrogen bonds: A:S.228 SO4.3: 2 residues within 4Å: Chain A: R.74, R.76 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Water bridges: A:R.74, B:G.72 Salt bridges: A:R.74, A:R.76 SO4.6: 2 residues within 4Å: Chain B: R.74, R.76 4 PLIP interactions: 4 interactions with chain B Water bridges: B:R.76, B:R.76 Salt bridges: B:R.74, B:R.76 SO4.7: 3 residues within 4Å: Chain B: E.284, R.286, H.316 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:R.286, B:H.316

2 x FFO: N-[4-({[(6S)-2-amino-5-formyl-4-oxo-3,4,5,6,7,8-hexahydropteridin-6-yl]methyl}amino)benzoyl]-L-glutamic acid(Non-covalent)

FFO.4: 13 residues within 4Å: Chain A: F.92, I.120, W.121, N.124, L.204, C.207, D.230, L.233, G.234, F.237, N.238, M.323, A.324 19 PLIP interactions: 19 interactions with chain A Hydrophobic interactions: A:F.92, A:I.120, A:I.120, A:I.120, A:L.233 Hydrogen bonds: A:N.124, A:N.238, A:A.324, A:A.324 Water bridges: A:R.62, A:K.89, A:N.124, A:Y.147, A:Q.226, A:I.319, A:M.323 Salt bridges: A:K.89, A:D.230 pi-Stacking: A:F.237 FFO.8: 14 residues within 4Å: Chain B: F.92, I.120, W.121, N.124, L.204, C.207, D.230, L.233, G.234, F.237, N.238, M.323, A.324 Ligands: GOL.9 17 PLIP interactions: 17 interactions with chain B Hydrophobic interactions: B:I.120, B:I.120, B:I.120 Hydrogen bonds: B:N.124, B:N.238, B:A.324, B:A.324 Water bridges: B:R.62, B:E.99, B:N.124, B:Q.226, B:D.230, B:M.321, B:M.321 Salt bridges: B:K.89, B:D.230 pi-Stacking: B:F.237

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

CL.5: 3 residues within 4Å: Chain A: R.90, P.317, T.318 Ligand excluded by PLIP CL.10: 2 residues within 4Å: Chain B: R.90, T.318 Ligand excluded by PLIP CL.11: 3 residues within 4Å: Chain B: F.135, T.137, R.138 Ligand excluded by PLIP

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.9: 2 residues within 4Å: Chain B: F.92 Ligands: FFO.8 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pozzi, C. et al., Evidence of Destabilization of the Human Thymidylate Synthase (hTS) Dimeric Structure Induced by the Interface Mutation Q62R. Biomolecules (2019)

Release Date

2019-04-10

Peptides

Thymidylate synthase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

Thymidylate synthase

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