SMTL ID : 3onn.1

Crystal structure of 5'-nucleotidase SDT1 from saccharomyces cerevisiae

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.87 Å

Oligo State

monomer

Ligands

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

PO4.1: 8 residues within 4Å: Chain A: D.36, I.37, D.38, T.140, N.141, A.142, K.177 Ligands: MG.13 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:I.37, A:D.38, A:D.38, A:D.38, A:D.38, A:T.140, A:N.141, A:A.142 Water bridges: A:K.177 Salt bridges: A:K.177

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 2 residues within 4Å: Chain A: L.256 Ligands: GOL.3 1 PLIP interactions: 1 interactions with chain A Water bridges: A:E.257 GOL.3: 2 residues within 4Å: Chain A: E.257 Ligands: GOL.2 2 PLIP interactions: 2 interactions with chain A Water bridges: A:E.257, A:E.257 GOL.4: 4 residues within 4Å: Chain A: R.128, I.133, D.134, K.135 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.128, A:R.128, A:D.134 Water bridges: A:S.130 GOL.5: 5 residues within 4Å: Chain A: S.44, V.223, E.224, N.225, E.226 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:S.44, A:E.224, A:N.225, A:N.225 Water bridges: A:E.226, A:E.226 GOL.6: 6 residues within 4Å: Chain A: T.46, I.113, L.114, K.115, P.116, D.117 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.115, A:K.115, A:P.116

2 x ACT: ACETATE ION(Non-functional Binders)

ACT.7: 6 residues within 4Å: Chain A: L.51, S.55, R.58, S.107, L.108, P.109 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.51 Hydrogen bonds: A:S.55 Salt bridges: A:R.58 ACT.8: 6 residues within 4Å: Chain A: G.205, K.206, E.209, G.232, Q.233, P.235 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:K.206 Hydrogen bonds: A:Q.233 Water bridges: A:E.236 Salt bridges: A:K.206

4 x IOD: IODIDE ION(Non-functional Binders)

IOD.9: 1 residues within 4Å: Chain A: N.96 Ligand excluded by PLIP IOD.10: 3 residues within 4Å: Chain A: L.3, Q.111, R.149 Ligand excluded by PLIP IOD.11: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP IOD.12: 3 residues within 4Å: Chain A: D.167, V.175, K.185 Ligand excluded by PLIP

1 x MG: MAGNESIUM ION(Non-covalent)

MG.13: 5 residues within 4Å: Chain A: D.36, D.38, D.202, D.203 Ligands: PO4.1 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.36, A:D.38, A:D.203, H2O.7, H2O.7

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Shi, N. et al., Crystal structure of the first pyrimidine 5'-nucleotidase SDT1 from saccharomyces cerevisiae. To be Published

Release Date

2011-03-02

Peptides

Protein SSM1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Protein SSM1