SMTL ID : 2a9w.2 (1 other biounit)

E. coli TS complexed with dUMP and inhibitor GA9

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.65 Å

Oligo State

homo-dimer

Ligands

6 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.1: 5 residues within 4Å: Chain A: R.21, R.166 Chain B: R.126, R.127 Ligands: UMP.4 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:R.21, B:R.126 Salt bridges: A:R.166 Water bridges: B:R.127 PO4.2: 3 residues within 4Å: Chain A: E.223, R.225, H.255 4 PLIP interactions: 4 interactions with chain A Water bridges: A:E.223, A:E.223 Salt bridges: A:R.225, A:H.255 PO4.3: 4 residues within 4Å: Chain A: Q.215, K.259, P.261 Ligands: GOL.7 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.259 PO4.9: 6 residues within 4Å: Chain A: R.126, R.127 Chain B: R.21, R.166, S.167 Ligands: UMP.12 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:S.167, A:R.126 Water bridges: B:R.21 Salt bridges: B:R.166 PO4.10: 3 residues within 4Å: Chain B: E.223, R.225, H.255 4 PLIP interactions: 4 interactions with chain B Water bridges: B:E.223, B:E.223 Salt bridges: B:R.225, B:H.255 PO4.11: 3 residues within 4Å: Chain B: Q.215, P.261 Ligands: GOL.15 No protein-ligand interaction detected (PLIP)

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

UMP.4: 14 residues within 4Å: Chain A: R.21, C.146, H.147, Q.165, R.166, S.167, C.168, D.169, H.207, Y.209 Chain B: R.126 Ligands: PO4.1, GA9.5, BME.6 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:Q.165, A:S.167, A:D.169 Water bridges: A:G.173 Salt bridges: A:R.166, B:R.126 UMP.12: 13 residues within 4Å: Chain A: R.126 Chain B: C.146, H.147, Q.165, R.166, S.167, C.168, D.169, H.207, Y.209 Ligands: PO4.9, GA9.13, BME.14 8 PLIP interactions: 1 interactions with chain A, 7 interactions with chain B Salt bridges: A:R.126, B:R.166 Hydrogen bonds: B:H.147, B:Q.165, B:S.167, B:D.169, B:H.207, B:Y.209

2 x GA9: 3,3-BIS(3-BROMO-4-HYDROXYPHENYL)-7-CHLORO-1H,3H-BENZO[DE]ISOCHROMEN-1-ONE(Non-covalent)

GA9.5: 9 residues within 4Å: Chain A: H.51, S.54, I.79, L.172, G.173, F.176, A.260 Ligands: UMP.4, GOL.8 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:I.79 Hydrogen bonds: A:S.54, A:E.82 Water bridges: A:S.54 Halogen bonds: A:H.51 GA9.13: 9 residues within 4Å: Chain B: H.51, S.54, I.79, L.172, G.173, F.176, A.260 Ligands: UMP.12, GOL.16 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:I.79, B:L.172, B:L.172 Hydrogen bonds: B:S.54 Water bridges: B:S.54, B:A.260 Halogen bonds: B:H.51

2 x BME: BETA-MERCAPTOETHANOL(Non-functional Binders)

BME.6: 7 residues within 4Å: Chain A: Q.165, S.167, C.168, D.169, G.173, L.174 Ligands: UMP.4 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.165 Water bridges: A:D.169 BME.14: 4 residues within 4Å: Chain B: C.146, R.166, S.167 Ligands: UMP.12 No protein-ligand interaction detected (PLIP)

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 6 residues within 4Å: Chain A: N.211, H.212, M.213, D.214, Q.215 Ligands: PO4.3 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.210, A:M.213, A:D.214, A:Q.215 GOL.8: 7 residues within 4Å: Chain A: L.44, C.50, H.51, I.55, P.175, F.176 Ligands: GA9.5 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.51 Water bridges: A:K.48 GOL.15: 7 residues within 4Å: Chain B: S.210, N.211, H.212, M.213, D.214, Q.215 Ligands: PO4.11 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:S.210, B:M.213, B:D.214, B:D.214, B:Q.215, B:Q.215 GOL.16: 7 residues within 4Å: Chain B: K.48, C.50, H.51, I.55, P.175, F.176 Ligands: GA9.13 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.48

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Finer-Moore, J.S. et al., The structure of Cryptococcus neoformans thymidylate synthase suggests strategies for using target dynamics for species-specific inhibition. Acta Crystallogr.,Sect.D (2005)

Release Date

2005-10-11

Peptides

Thymidylate synthase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

Thymidylate synthase

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