SMTL ID : 5jfe.1

Flavin-dependent thymidylate synthase with H2-dUMP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.03 Å

Oligo State

homo-tetramer

Ligands

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

FAD.1: 23 residues within 4Å: Chain A: R.90, H.91, R.92, I.93, N.181, L.185, R.186, H.190 Chain B: T.67, E.70, I.93, N.175, R.177 Chain D: S.95, N.97, E.98, S.100, R.102, Y.103 Ligands: UMC.2, EDO.4, EDO.6, FAD.8 29 PLIP interactions: 17 interactions with chain A, 7 interactions with chain D, 5 interactions with chain B Hydrophobic interactions: A:L.185 Hydrogen bonds: A:R.90, A:R.90, A:R.92, A:R.92, A:I.93, A:N.181, A:N.181, D:S.95, D:E.98, D:E.98, D:S.100, B:N.175 Water bridges: A:R.90, A:H.91, A:H.91, A:R.92, A:R.92, D:A.94, D:Y.96, D:Y.96, B:T.67, B:R.177, B:R.177 Salt bridges: A:H.91, A:H.91, A:R.92, A:R.92, B:R.177 FAD.8: 23 residues within 4Å: Chain A: T.67, E.70, I.93, N.175, R.177 Chain B: R.90, H.91, R.92, I.93, N.181, L.185, R.186, H.190 Chain C: S.95, N.97, E.98, S.100, R.102, Y.103 Ligands: FAD.1, UMC.9, EDO.11, EDO.13 28 PLIP interactions: 15 interactions with chain B, 7 interactions with chain C, 6 interactions with chain A Hydrophobic interactions: B:L.185 Hydrogen bonds: B:R.90, B:R.90, B:R.92, B:R.92, B:I.93, B:N.181, B:N.181, C:S.95, C:E.98, C:E.98, C:S.100, A:T.67, A:N.175 Water bridges: B:R.90, B:R.92, B:R.92, C:A.94, C:Y.96, C:Y.96, A:T.67, A:R.177, A:R.177 Salt bridges: B:H.91, B:H.91, B:R.92, B:R.92, A:R.177 FAD.15: 23 residues within 4Å: Chain B: S.95, N.97, E.98, S.100, R.102, Y.103 Chain C: R.90, H.91, R.92, I.93, N.181, L.185, R.186, H.190 Chain D: T.67, E.70, I.93, N.175, R.177 Ligands: UMC.16, EDO.18, EDO.20, FAD.22 29 PLIP interactions: 17 interactions with chain C, 7 interactions with chain B, 5 interactions with chain D Hydrophobic interactions: C:L.185 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, B:S.100, D:N.175 Water bridges: C:R.90, C:H.91, C:H.91, C:R.92, C:R.92, B:A.94, B:Y.96, B:Y.96, D:T.67, D:R.177, D:R.177 Salt bridges: C:H.91, C:H.91, C:R.92, C:R.92, D:R.177 FAD.22: 23 residues within 4Å: Chain A: S.95, N.97, E.98, S.100, R.102, Y.103 Chain C: 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: FAD.15, UMC.23, EDO.25, EDO.27 28 PLIP interactions: 15 interactions with chain D, 7 interactions with chain A, 6 interactions with chain C Hydrophobic interactions: D:L.185 Hydrogen bonds: D:R.90, D:R.90, D:R.92, D:R.92, D:I.93, D:N.181, D:N.181, A:S.95, A:E.98, A:E.98, A:S.100, C:T.67, C:N.175 Water bridges: D:R.90, D:R.92, D:R.92, A:A.94, A:Y.96, A:Y.96, C:T.67, C:R.177, C:R.177 Salt bridges: D:H.91, D:H.91, D:R.92, D:R.92, C:R.177

4 x UMC: 2'-deoxy-5'-uridylic acid(Non-covalent)

UMC.2: 13 residues within 4Å: Chain A: R.86, Q.87, R.90, R.186 Chain D: F.89, E.98, L.99, S.100, G.101, R.102, R.159 Ligands: FAD.1, EDO.3 17 PLIP interactions: 8 interactions with chain D, 9 interactions with chain A Hydrogen bonds: D:E.98, D:G.101, D:R.102, D:R.102, A:Q.87, A:R.90, A:R.186, A:R.186 Water bridges: D:R.159, D:R.159, D:R.159, A:R.86, A:R.86, A:Q.87, A:Q.192 Salt bridges: D:R.159 Hydrophobic interactions: A:R.90 UMC.9: 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, R.159 Ligands: FAD.8, EDO.10 16 PLIP interactions: 9 interactions with chain B, 7 interactions with chain C Hydrophobic interactions: B:R.90 Hydrogen bonds: B:Q.87, B:R.90, B:R.186, B:R.186, C:G.101, C:R.102, C:R.102 Water bridges: B:R.86, B:R.86, B:Q.87, B:Q.192, C:R.159, C:R.159, C:R.159 Salt bridges: C:R.159 UMC.16: 13 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.15, EDO.17 17 PLIP interactions: 9 interactions with chain C, 8 interactions with chain B Hydrophobic interactions: C:R.90 Hydrogen bonds: C:Q.87, C:R.90, C:R.186, C:R.186, B:E.98, B:G.101, B:R.102, B:R.102 Water bridges: C:R.86, C:R.86, C:Q.87, C:Q.192, B:R.159, B:R.159, B:R.159 Salt bridges: B:R.159 UMC.23: 13 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.22, EDO.24 16 PLIP interactions: 9 interactions with chain D, 7 interactions with chain A Hydrophobic interactions: D:R.90 Hydrogen bonds: D:Q.87, D:R.90, D:R.186, D:R.186, A:G.101, A:R.102, A:R.102 Water bridges: D:R.86, D:R.86, D:Q.87, D:Q.192, A:R.159, A:R.159, A:R.159 Salt bridges: A:R.159

20 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.3: 6 residues within 4Å: Chain D: L.99, G.101, L.106, R.159, T.168 Ligands: UMC.2 Ligand excluded by PLIP EDO.4: 6 residues within 4Å: Chain B: H.65, T.67, P.68 Chain D: N.97 Ligands: FAD.1, EDO.6 Ligand excluded by PLIP EDO.5: 3 residues within 4Å: Chain A: I.125, R.129, K.133 Ligand excluded by PLIP EDO.6: 5 residues within 4Å: Chain B: Y.59, H.65 Chain D: Y.103 Ligands: FAD.1, EDO.4 Ligand excluded by PLIP EDO.7: 4 residues within 4Å: Chain A: K.105, Y.108, Y.142, L.146 Ligand excluded by PLIP EDO.10: 6 residues within 4Å: Chain C: L.99, G.101, L.106, R.159, T.168 Ligands: UMC.9 Ligand excluded by PLIP EDO.11: 6 residues within 4Å: Chain A: H.65, T.67, P.68 Chain C: N.97 Ligands: FAD.8, EDO.13 Ligand excluded by PLIP EDO.12: 3 residues within 4Å: Chain B: I.125, R.129, K.133 Ligand excluded by PLIP EDO.13: 5 residues within 4Å: Chain A: Y.59, H.65 Chain C: Y.103 Ligands: FAD.8, EDO.11 Ligand excluded by PLIP EDO.14: 4 residues within 4Å: Chain B: K.105, Y.108, Y.142, L.146 Ligand excluded by PLIP EDO.17: 6 residues within 4Å: Chain B: L.99, G.101, L.106, R.159, T.168 Ligands: UMC.16 Ligand excluded by PLIP EDO.18: 6 residues within 4Å: Chain B: N.97 Chain D: H.65, T.67, P.68 Ligands: FAD.15, EDO.20 Ligand excluded by PLIP EDO.19: 3 residues within 4Å: Chain C: I.125, R.129, K.133 Ligand excluded by PLIP EDO.20: 5 residues within 4Å: Chain B: Y.103 Chain D: Y.59, H.65 Ligands: FAD.15, EDO.18 Ligand excluded by PLIP EDO.21: 4 residues within 4Å: Chain C: K.105, Y.108, Y.142, L.146 Ligand excluded by PLIP EDO.24: 6 residues within 4Å: Chain A: L.99, G.101, L.106, R.159, T.168 Ligands: UMC.23 Ligand excluded by PLIP EDO.25: 6 residues within 4Å: Chain A: N.97 Chain C: H.65, T.67, P.68 Ligands: FAD.22, EDO.27 Ligand excluded by PLIP EDO.26: 3 residues within 4Å: Chain D: I.125, R.129, K.133 Ligand excluded by PLIP EDO.27: 5 residues within 4Å: Chain A: Y.103 Chain C: Y.59, H.65 Ligands: FAD.22, EDO.25 Ligand excluded by PLIP EDO.28: 4 residues within 4Å: Chain D: K.105, Y.108, Y.142, L.146 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sapra, A. et al., Evaluating H2-dUMP as an Intermediate in the oxidation of Flavin-dependent Thymidylate Synthase. To Be Published

Release Date

2017-04-26

Peptides

Thymidylate synthase ThyX: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

Thymidylate synthase ThyX

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