SMTL ID : 1ddu.1

E. COLI THYMIDYLATE SYNTHASE IN COMPLEX WITH CB3717 AND 2',5'-DIDEOXYURIDINE (DDURD)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-dimer

Ligands

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

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

2 x DDU: 2'-5'DIDEOXYURIDINE(Non-covalent)

DDU.2: 12 residues within 4Å: Chain A: C.147, H.148, Q.166, S.168, C.169, D.170, G.174, N.178, H.208, Y.210 Ligands: PO4.1, CB3.3 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Q.166, A:D.170, A:N.178, A:N.178, A:H.208 DDU.5: 13 residues within 4Å: Chain A: R.127 Chain B: C.147, H.148, Q.166, S.168, C.169, D.170, G.174, N.178, H.208, Y.210 Ligands: PO4.4, CB3.6 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:Q.166, B:D.170, B:N.178, B:N.178, B:H.208, B:Y.210

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

CB3.3: 15 residues within 4Å: Chain A: K.49, E.59, I.80, W.84, L.144, D.170, L.173, G.174, F.177, N.178, Y.210, K.260, V.263, A.264 Ligands: DDU.2 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:I.80, A:W.84, A:L.144, A:L.173, A:F.177 Hydrogen bonds: A:A.264, 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: DDU.5 16 PLIP interactions: 16 interactions with chain B Hydrophobic interactions: B:I.80, B:I.80, B:W.84, B:W.84, B:F.177, B:F.177, B:F.177 Hydrogen bonds: B:S.55, B:Y.210, B:A.264, 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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