SMTL ID : 4kx3.1

Structure of murine cytosolic 5'-nucleotidase III complexed with thymidine monophosphate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

monomer

Ligands

1 x DT: THYMIDINE-5'-MONOPHOSPHATE(Non-covalent)

DT.1: 17 residues within 4Å: Chain A: D.49, F.50, N.51, T.66, H.68, N.69, E.96, W.113, Y.114, S.117, S.164, A.165, G.166, V.210, K.213 Ligands: MG.2, EDO.4 20 PLIP interactions: 20 interactions with chain A Hydrophobic interactions: A:W.113, A:Y.114, A:V.210 Hydrogen bonds: A:D.49, A:D.49, A:F.50, A:N.51, A:N.51, A:T.66, A:N.69, A:S.117, A:A.165 Water bridges: A:D.72, A:D.72, A:D.72, A:E.96, A:K.213 Salt bridges: A:K.213 pi-Stacking: A:H.68, A:W.113

1 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: D.49, N.51, D.238 Ligands: DT.1 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.49, A:N.51, A:D.238, H2O.1, H2O.1

4 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.3: 3 residues within 4Å: Chain A: T.27, R.28, E.31 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.28 EDO.4: 7 residues within 4Å: Chain A: R.63, T.66, N.69, K.89, Y.93, W.113 Ligands: DT.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.63, A:N.69 EDO.5: 3 residues within 4Å: Chain A: E.172, R.176, Y.181 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.176, A:R.176, A:Y.181 EDO.9: 6 residues within 4Å: Chain A: A.41, A.42, H.156, G.157, P.159, N.230 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.156, A:N.230, A:N.230

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

BME.6: 5 residues within 4Å: Chain A: A.7, V.8, C.34, I.37, K.38 No protein-ligand interaction detected (PLIP) BME.7: 5 residues within 4Å: Chain A: Y.59, K.62, R.63, C.64, D.139 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.59

1 x EPE: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID(Non-functional Binders)

EPE.8: 3 residues within 4Å: Chain A: Q.294, K.295, L.297 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.294

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bitto, E. et al., Structure of murine cytosolic 5'-nucleotidase III complexed with thymidine monophosphate. To be Published

Release Date

2013-06-05

Peptides

Cytosolic 5'-nucleotidase 3: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Cytosolic 5'-nucleotidase 3