SMTL ID : 4lrr.1

Ternary complex between E. coli thymidylate synthase, dUMP, and F9

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.41 Å

Oligo State

homo-dimer

Ligands

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

SO4.1: 2 residues within 4Å: Chain A: L.219, R.223 Ligand excluded by PLIP SO4.2: 3 residues within 4Å: Chain A: E.224, R.226, H.256 Ligand excluded by PLIP SO4.3: 3 residues within 4Å: Chain A: R.226, P.255, P.257 Ligand excluded by PLIP SO4.4: 3 residues within 4Å: Chain A: I.250, E.251, G.252 Ligand excluded by PLIP SO4.5: 3 residues within 4Å: Chain A: H.52, R.54, S.55 Ligand excluded by PLIP SO4.6: 2 residues within 4Å: Chain A: N.20 Ligands: SO4.8 Ligand excluded by PLIP SO4.7: 3 residues within 4Å: Chain A: R.50, P.257, G.258 Ligand excluded by PLIP SO4.8: 3 residues within 4Å: Chain A: G.26, S.211 Ligands: SO4.6 Ligand excluded by PLIP SO4.11: 2 residues within 4Å: Chain B: L.219, R.223 Ligand excluded by PLIP SO4.12: 3 residues within 4Å: Chain B: E.224, R.226, H.256 Ligand excluded by PLIP SO4.13: 3 residues within 4Å: Chain B: R.226, P.255, P.257 Ligand excluded by PLIP SO4.14: 3 residues within 4Å: Chain B: I.250, E.251, G.252 Ligand excluded by PLIP SO4.15: 3 residues within 4Å: Chain B: H.52, R.54, S.55 Ligand excluded by PLIP SO4.16: 2 residues within 4Å: Chain B: N.20 Ligands: SO4.18 Ligand excluded by PLIP SO4.17: 3 residues within 4Å: Chain B: R.50, P.257, G.258 Ligand excluded by PLIP SO4.18: 3 residues within 4Å: Chain B: G.26, S.211 Ligands: SO4.16 Ligand excluded by PLIP

2 x CF9: 2-OXO-2H-NAPHTHO[1,8-BC]FURAN-6-YL 4-NITROBENZOATE(Non-covalent)

CF9.9: 16 residues within 4Å: Chain A: E.59, F.63, I.80, W.81, W.84, Y.95, L.144, C.147, H.148, Q.166, S.168, C.169, D.170, G.174, L.175, N.178 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:I.80, A:W.81, A:W.84, A:L.144, A:D.170 Salt bridges: A:H.148 CF9.19: 16 residues within 4Å: Chain B: E.59, F.63, I.80, W.81, W.84, Y.95, L.144, C.147, H.148, Q.166, S.168, C.169, D.170, G.174, L.175, N.178 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:I.80, B:W.81, B:W.84, B:L.144, B:D.170 Salt bridges: B:H.148

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

UMP.10: 7 residues within 4Å: Chain A: R.22, R.167, S.168 Chain B: D.123, S.126, R.127, R.128 8 PLIP interactions: 4 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:R.128 Hydrogen bonds: B:R.127, A:R.22, A:S.168 Water bridges: B:D.125 Salt bridges: B:R.127, A:R.22, A:R.167 UMP.20: 7 residues within 4Å: Chain A: D.123, S.126, R.127, R.128 Chain B: R.22, R.167, S.168 8 PLIP interactions: 4 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:R.22, B:S.168, A:R.127 Salt bridges: B:R.22, B:R.167, A:R.127 Hydrophobic interactions: A:R.128 Water bridges: A:D.125

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ferrari, S. et al., 2'-Deoxyuridine 5'-Monophosphate Substrate Displacement in Thymidylate Synthase through 6-Hydroxy-2H-naphtho[1,8-bc]furan-2-one Derivatives. J.Med.Chem. (2013)

Release Date

2013-11-06

Peptides

Thymidylate synthase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Thymidylate synthase

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