SMTL ID : 5x66.2 (2 other biounits)

Human thymidylate synthase in complex with dUMP and methotrexate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.99 Å

Oligo State

homo-dimer

Ligands

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

UMP.1: 15 residues within 4Å: Chain A: R.27, C.172, H.173, Q.191, R.192, S.193, G.194, D.195, G.199, N.203, H.233, Y.235 Chain B: R.152, R.153 Ligands: MTX.2 14 PLIP interactions: 12 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:D.195 Hydrogen bonds: A:Q.191, A:S.193, A:D.195, A:N.203, A:N.203, A:H.233, A:Y.235 Water bridges: A:R.27, A:R.27 Salt bridges: A:R.27, A:R.192, B:R.152, B:R.153 UMP.3: 14 residues within 4Å: Chain A: R.152, R.153 Chain B: C.172, H.173, Q.191, R.192, S.193, G.194, D.195, G.199, N.203, H.233, Y.235 Ligands: MTX.4 11 PLIP interactions: 9 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:D.195 Hydrogen bonds: B:Q.191, B:S.193, B:D.195, B:N.203, B:N.203, B:H.233, B:Y.235 Salt bridges: B:R.192, A:R.152, A:R.153

2 x MTX: METHOTREXATE(Non-covalent)

MTX.2: 13 residues within 4Å: Chain A: R.55, F.57, I.85, D.195, L.198, G.199, F.202, N.203, Y.235, T.283, M.288, A.289 Ligands: UMP.1 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:F.57, A:I.85, A:I.85, A:F.202 Hydrogen bonds: A:F.57, A:D.195, A:A.289, A:A.289 Salt bridges: A:K.54, A:D.195 MTX.4: 14 residues within 4Å: Chain B: F.57, G.82, V.83, K.84, I.85, D.195, L.198, G.199, F.202, N.203, Y.235, M.288, A.289 Ligands: UMP.3 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:I.85, B:I.85 Hydrogen bonds: B:K.84, B:D.195, B:Y.235, B:Y.235, B:A.289 Salt bridges: B:D.195 pi-Stacking: B:F.202

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chen, D. et al., Structural analyses of human thymidylate synthase reveal a site that may control conformational switching between active and inactive states. J. Biol. Chem. (2017)

Release Date

2017-06-28

Peptides

Thymidylate synthase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
E

Thymidylate synthase

Related Entries With Identical Sequence