SMTL ID : 3ah5.2 (1 other biounit)

Crystal Structure of flavin dependent thymidylate synthase ThyX from helicobacter pylori complexed with FAD and dUMP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-tetramer

Ligands

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

UMP.1: 12 residues within 4Å: Chain A: Q.70, E.71, R.74, R.174 Chain D: R.66, L.69, V.82, S.84, S.85, R.86, K.147 Ligands: FAD.9 18 PLIP interactions: 8 interactions with chain A, 10 interactions with chain D Hydrophobic interactions: A:R.74 Hydrogen bonds: A:E.71, A:R.74, A:R.174, A:R.174, D:S.84, D:S.85, D:R.86, D:R.86 Water bridges: A:Q.70, A:E.71, A:L.180, D:R.66, D:S.73, D:S.85, D:K.147 Salt bridges: D:R.66, D:K.147 UMP.6: 10 residues within 4Å: Chain B: Q.70, E.71, R.74, R.174 Chain C: R.66, L.69, S.84, S.85, R.86 Ligands: FAD.12 16 PLIP interactions: 8 interactions with chain B, 8 interactions with chain C Hydrophobic interactions: B:R.74 Hydrogen bonds: B:Q.70, B:R.74, B:R.174, B:R.174, C:S.84, C:S.85, C:R.86, C:R.86 Water bridges: B:E.71, B:E.71, B:E.71, C:R.66, C:S.73 Salt bridges: C:R.66, C:K.147 UMP.8: 12 residues within 4Å: Chain B: R.66, L.69, V.82, S.84, S.85, R.86, K.147 Chain C: Q.70, E.71, R.74, R.174 Ligands: FAD.2 19 PLIP interactions: 11 interactions with chain B, 8 interactions with chain C Hydrogen bonds: B:S.84, B:S.85, B:R.86, B:R.86, C:E.71, C:E.71, C:R.74, C:R.174, C:R.174 Water bridges: B:R.66, B:S.73, B:S.73, B:S.85, B:K.147, C:E.71, C:L.180 Salt bridges: B:R.66, B:K.147 Hydrophobic interactions: C:R.74 UMP.13: 10 residues within 4Å: Chain A: R.66, L.69, S.84, S.85, R.86 Chain D: Q.70, E.71, R.74, R.174 Ligands: FAD.5 17 PLIP interactions: 8 interactions with chain D, 9 interactions with chain A Hydrophobic interactions: D:R.74 Hydrogen bonds: D:Q.70, D:E.71, D:R.74, D:R.174, D:R.174, A:S.84, A:S.85, A:R.86, A:R.86 Water bridges: D:E.71, D:E.71, A:R.66, A:S.73, A:K.147 Salt bridges: A:R.66, A:K.147

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

FAD.2: 24 residues within 4Å: Chain A: C.21, R.47, H.48, S.50, E.53, I.77, N.163, R.165 Chain B: S.79, L.80, S.81, V.82, S.84, Y.87 Chain C: R.74, H.75, R.76, I.77, N.169, L.173, R.174, K.178 Ligands: UMP.8, FAD.9 22 PLIP interactions: 9 interactions with chain A, 10 interactions with chain C, 3 interactions with chain B Hydrogen bonds: A:R.47, A:S.50, A:N.163, A:R.165, A:R.165, C:R.74, C:R.74, C:R.76, C:R.76, C:I.77, C:N.169, C:N.169, C:R.174, B:S.79, B:V.82, B:V.82 Water bridges: A:S.50, A:R.165, A:R.165 Salt bridges: A:R.165, C:H.75, C:H.75 FAD.5: 25 residues within 4Å: Chain A: S.79, L.80, S.81, V.82, S.84, Y.87 Chain B: C.21, F.46, R.47, H.48, S.50, E.53, I.77, N.163, R.165 Chain D: R.74, H.75, R.76, I.77, N.169, L.173, R.174, K.178 Ligands: FAD.12, UMP.13 23 PLIP interactions: 11 interactions with chain D, 8 interactions with chain B, 4 interactions with chain A Hydrogen bonds: D:R.74, D:R.74, D:R.76, D:R.76, D:I.77, D:N.169, D:R.174, B:R.47, B:R.47, B:S.50, B:S.50, B:N.163, B:R.165, B:R.165, A:S.79, A:V.82, A:V.82 Salt bridges: D:H.75, D:H.75, D:R.76, D:R.76, B:R.165 Water bridges: A:S.84 FAD.9: 24 residues within 4Å: Chain A: R.74, H.75, R.76, I.77, N.169, L.173, R.174, K.178 Chain C: C.21, R.47, H.48, S.50, E.53, I.77, N.163, R.165 Chain D: S.79, L.80, S.81, V.82, S.84, Y.87 Ligands: UMP.1, FAD.2 24 PLIP interactions: 10 interactions with chain C, 4 interactions with chain D, 10 interactions with chain A Hydrogen bonds: C:R.47, C:S.50, C:E.53, C:N.163, C:R.165, C:R.165, D:S.79, D:V.82, D:V.82, D:Y.87, A:R.74, A:R.74, A:R.76, A:R.76, A:I.77, A:N.169, A:N.169, A:R.174 Water bridges: C:S.50, C:R.165, C:R.165 Salt bridges: C:R.165, A:H.75, A:H.75 FAD.12: 25 residues within 4Å: Chain B: R.74, H.75, R.76, I.77, N.169, L.173, R.174, K.178 Chain C: S.79, L.80, S.81, V.82, S.84, Y.87 Chain D: C.21, F.46, R.47, H.48, S.50, E.53, I.77, N.163, R.165 Ligands: FAD.5, UMP.6 24 PLIP interactions: 5 interactions with chain C, 8 interactions with chain D, 11 interactions with chain B Hydrogen bonds: C:S.79, C:V.82, C:V.82, C:Y.87, D:R.47, D:R.47, D:S.50, D:S.50, D:N.163, D:R.165, D:R.165, B:R.74, B:R.74, B:R.76, B:R.76, B:I.77, B:N.169, B:R.174 Water bridges: C:S.84 Salt bridges: D:R.165, B:H.75, B:H.75, B:R.76, B:R.76

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

SO4.3: 2 residues within 4Å: Chain A: P.195, G.196 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.196 SO4.4: 3 residues within 4Å: Chain A: L.99, P.100, L.101 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:L.101 SO4.7: 2 residues within 4Å: Chain B: P.195, G.196 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:G.196 SO4.10: 2 residues within 4Å: Chain C: P.195, G.196 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:G.196 SO4.11: 3 residues within 4Å: Chain C: L.99, P.100, L.101 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:L.101 SO4.14: 2 residues within 4Å: Chain D: P.195, G.196 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:G.196

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhang, X. et al., Crystal structure and functional analysis of a flavin dependent thymidylate synthase from helicobacter pylori. To be Published

Release Date

2011-04-20

Peptides

Thymidylate synthase thyX: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
E

B
F

C
E

D
F

Thymidylate synthase thyX

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