SMTL ID : 1tdu.1

E. COLI THYMIDYLATE SYNTHASE IN COMPLEX WITH CB3717 AND 2'-DEOXYURIDINE (DURD)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-dimer

Ligands

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

PO4.1: 7 residues within 4Å: Chain A: R.22, L.144, R.167, S.168 Chain B: R.127, R.128 Ligands: DUR.3 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:S.168 Salt bridges: A:R.22, A:R.167, B:R.127, B:R.128 PO4.2: 8 residues within 4Å: Chain A: R.127, R.128 Chain B: R.22, L.144, A.145, R.167, S.168 Ligands: DUR.5 6 PLIP interactions: 3 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:S.168, A:R.127 Salt bridges: B:R.22, B:R.167, A:R.128 Water bridges: A:R.127

2 x DUR: 2'-DEOXYURIDINE(Non-covalent)

DUR.3: 13 residues within 4Å: Chain A: L.144, C.147, H.148, Q.166, S.168, C.169, D.170, G.174, N.178, H.208, Y.210 Ligands: PO4.1, CB3.4 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Q.166, A:D.170, A:N.178, A:N.178, A:H.208 Water bridges: A:A.145 DUR.5: 14 residues within 4Å: Chain A: R.127 Chain B: L.144, C.147, H.148, Q.166, S.168, C.169, D.170, G.174, N.178, H.208, Y.210 Ligands: PO4.2, CB3.6 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:Q.166, B:D.170, B:N.178, B:N.178, B:H.208, B:Y.210 Water bridges: B:Y.95, B:A.145

2 x CB3: 10-PROPARGYL-5,8-DIDEAZAFOLIC ACID(Non-covalent)

CB3.4: 18 residues within 4Å: Chain A: K.49, R.50, C.51, H.52, E.59, I.80, W.81, W.84, D.170, L.173, G.174, F.177, N.178, Y.210, K.260, V.263, A.264 Ligands: DUR.3 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:I.80, A:W.81, A:W.84, A:W.84, A:F.177, A:F.177, A:F.177 Hydrogen bonds: A:H.52, A:A.264, A:A.264 Salt bridges: A:K.49, A:D.170, A:K.260 CB3.6: 13 residues within 4Å: Chain B: H.52, S.55, E.59, I.80, W.84, D.170, L.173, G.174, F.177, N.178, Y.210, A.264 Ligands: DUR.5 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:I.80, B:I.80, B:W.84, B:W.84, B:F.177, B:F.177 Hydrogen bonds: B:S.55, B:Y.210, B:A.264, B:A.264 Salt bridges: B:K.49, B:H.52, B:H.52, B:D.170

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Stout, T.J. et al., The additivity of substrate fragments in enzyme-ligand binding. Structure (1998)

Release Date

1998-07-01

Peptides

THYMIDYLATE SYNTHASE: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

THYMIDYLATE SYNTHASE

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