SMTL ID : 4eb4.3 (2 other biounits)

Crystal structure of mouse thymidylate synthase in ternary complex with dUMP and Tomudex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.74 Å

Oligo State

homo-tetramer

Ligands

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

UMP.1: 16 residues within 4Å: Chain A: R.44, L.186, C.189, H.190, Q.208, R.209, S.210, G.211, D.212, G.216, N.220, H.250, Y.252 Chain B: R.169, R.170 Ligands: D16.2 13 PLIP interactions: 10 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:Q.208, A:S.210, A:S.210, A:D.212, A:N.220, A:N.220, A:H.250 Water bridges: A:H.190, B:R.169 Salt bridges: A:R.44, A:R.209, B:R.169, B:R.170 UMP.9: 16 residues within 4Å: Chain A: R.169, R.170 Chain B: R.44, L.186, C.189, H.190, Q.208, R.209, S.210, G.211, D.212, G.216, N.220, H.250, Y.252 Ligands: D16.10 12 PLIP interactions: 3 interactions with chain A, 9 interactions with chain B Water bridges: A:R.169 Salt bridges: A:R.169, A:R.170, B:R.44, B:R.209 Hydrogen bonds: B:Q.208, B:S.210, B:D.212, B:N.220, B:N.220, B:H.250, B:Y.252 UMP.15: 16 residues within 4Å: Chain C: R.44, C.189, H.190, Q.208, R.209, S.210, G.211, D.212, G.216, V.217, N.220, H.250, Y.252 Chain D: R.169, R.170 Ligands: D16.16 13 PLIP interactions: 11 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:Q.208, C:S.210, C:S.210, C:D.212, C:N.220, C:N.220, C:H.250, C:Y.252 Water bridges: C:H.190 Salt bridges: C:R.44, C:R.209, D:R.169, D:R.170 UMP.18: 15 residues within 4Å: Chain C: R.169, R.170 Chain D: R.44, C.189, H.190, Q.208, R.209, S.210, G.211, D.212, G.216, N.220, H.250, Y.252 Ligands: D16.19 10 PLIP interactions: 8 interactions with chain D, 2 interactions with chain C Hydrogen bonds: D:Q.208, D:S.210, D:D.212, D:N.220, D:N.220, D:H.250 Salt bridges: D:R.44, D:R.209, C:R.169, C:R.170

4 x D16: TOMUDEX(Non-covalent)

D16.2: 17 residues within 4Å: Chain A: F.74, I.102, W.103, N.106, D.212, L.215, G.216, F.219, N.220, Y.252, I.301, K.302, M.303, E.304, M.305, A.306 Ligands: UMP.1 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:I.102, A:I.102, A:W.103, A:L.215, A:Y.252, A:A.306 Hydrogen bonds: A:G.216, A:M.303, A:A.306 Water bridges: A:F.219, A:K.302, A:K.302, A:A.306 pi-Stacking: A:F.219 D16.10: 16 residues within 4Å: Chain B: F.74, I.102, W.103, N.106, D.212, L.215, G.216, F.219, N.220, Y.252, I.301, K.302, M.303, M.305, A.306 Ligands: UMP.9 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:I.102, B:I.102, B:W.103, B:L.215, B:Y.252, B:A.306 Hydrogen bonds: B:G.216, B:M.303 Water bridges: B:F.219, B:I.301, B:I.301, B:A.306, B:A.306 pi-Stacking: B:F.219 D16.16: 10 residues within 4Å: Chain C: F.74, R.101, I.102, D.212, L.215, G.216, F.219, N.220, Y.252 Ligands: UMP.15 9 PLIP interactions: 9 interactions with chain C Hydrophobic interactions: C:F.74, C:F.219, C:Y.252 Hydrogen bonds: C:D.212, C:G.216 Water bridges: C:F.74, C:R.101 Salt bridges: C:R.101 pi-Stacking: C:F.219 D16.19: 14 residues within 4Å: Chain D: F.74, I.102, W.103, D.212, L.215, G.216, F.219, N.220, Y.252, I.301, K.302, M.303, E.304 Ligands: UMP.18 11 PLIP interactions: 11 interactions with chain D Hydrophobic interactions: D:I.102, D:I.102, D:L.215, D:Y.252 Hydrogen bonds: D:D.212, D:G.216, D:M.303, D:E.304 Water bridges: D:R.72, D:I.301 pi-Stacking: D:F.219

1 x DTT: 2,3-DIHYDROXY-1,4-DITHIOBUTANE(Non-covalent)

DTT.3: 9 residues within 4Å: Chain A: Q.154, K.157, V.158, T.161, D.168, R.170, I.171, I.172 Chain B: W.176 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.157, A:T.161

10 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 6 residues within 4Å: Chain A: D.167, V.198, N.199 Chain B: K.40, K.41, E.42 7 PLIP interactions: 3 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:E.42, A:D.167, A:N.199 Water bridges: B:E.42, B:E.42, A:D.167, A:G.200 GOL.5: 7 residues within 4Å: Chain A: F.136, G.137, N.177, K.179 Chain B: G.137, N.177, K.179 7 PLIP interactions: 4 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:N.177, A:N.177, A:K.179, B:N.177, B:N.177 Water bridges: A:G.137, B:G.137 GOL.6: 3 residues within 4Å: Chain A: R.72, W.75, I.292 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.72 Water bridges: A:W.75, A:I.292, A:Y.295 GOL.7: 2 residues within 4Å: Chain A: R.277, K.278 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.278 Water bridges: A:L.276, A:K.278 GOL.11: 5 residues within 4Å: Chain B: L.115, L.181, P.182, M.184, P.187 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Water bridges: A:R.170 Hydrogen bonds: B:A.185 GOL.12: 6 residues within 4Å: Chain A: K.40, K.41, E.42 Chain B: D.167, V.198, N.199 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:N.199, A:E.42 Water bridges: B:D.167, B:D.167, B:G.200 GOL.13: 7 residues within 4Å: Chain B: H.22, G.23, E.24, L.25, P.267, R.268, P.269 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:H.22, B:E.24, B:L.25 Water bridges: B:P.267 GOL.17: 3 residues within 4Å: Chain C: R.21, H.22, R.58 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:R.21, C:R.58, C:S.60 Water bridges: C:R.58 GOL.20: 5 residues within 4Å: Chain D: R.36, C.37, G.38, F.39 Ligands: GOL.21 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:C.37 GOL.21: 4 residues within 4Å: Chain C: N.199 Chain D: F.39, K.40 Ligands: GOL.20 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:K.40

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

SO4.8: 4 residues within 4Å: Chain A: R.268, P.297, H.298, P.299 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.268, A:H.298

1 x MES: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID(Non-covalent)

MES.14: 5 residues within 4Å: Chain B: R.36, C.37, G.38, F.39, K.40 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.40 Water bridges: B:G.38

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dowiercial, A. et al., Crystal structure of mouse thymidylate synthase in tertiary complex with dUMP and raltitrexed reveals N-terminus architecture and two different active site conformations. Biomed Res Int (2014)

Release Date

2012-05-02

Peptides

Thymidylate synthase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Thymidylate synthase

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