SMTL ID : 2xje.1

Crystal structure of the D52N variant of cytosolic 5'-nucleotidase II in complex with uridine 5'-monophosphate and adenosine triphosphate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-dimer

Ligands

2 x U5P: URIDINE-5'-MONOPHOSPHATE(Non-covalent)

U5P.1: 15 residues within 4Å: Chain A: N.71, M.72, D.73, F.176, R.221, V.224, D.225, H.228, Y.229, K.234, T.268, N.269, S.270, K.311 Ligands: MG.5 19 PLIP interactions: 19 interactions with chain A Hydrophobic interactions: A:H.228, A:Y.229 Hydrogen bonds: A:N.71, A:M.72, A:D.73, A:D.73, A:R.221, A:R.221, A:H.228, A:Y.229, A:K.234, A:K.234, A:T.268, A:N.269, A:S.270 Water bridges: A:K.311, A:K.311 Salt bridges: A:K.311 pi-Stacking: A:H.228 U5P.6: 15 residues within 4Å: Chain B: N.71, M.72, D.73, F.176, R.221, V.224, D.225, H.228, Y.229, K.234, T.268, N.269, S.270, K.311 Ligands: MG.10 20 PLIP interactions: 20 interactions with chain B Hydrophobic interactions: B:H.228, B:Y.229 Hydrogen bonds: B:N.71, B:M.72, B:D.73, B:R.221, B:R.221, B:D.225, B:H.228, B:K.234, B:K.234, B:T.268, B:T.268, B:N.269, B:S.270 Water bridges: B:Y.229, B:K.311, B:K.311 Salt bridges: B:K.311 pi-Stacking: B:H.228

2 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.2: 13 residues within 4Å: Chain A: R.163, D.164, T.166, N.173, F.373, Q.472, R.475 Chain B: K.381, R.475, Y.476 Ligands: MG.4, ATP.7, MG.9 19 PLIP interactions: 6 interactions with chain B, 13 interactions with chain A Hydrogen bonds: B:R.475, B:Y.476, B:Y.476, A:R.163, A:R.163, A:N.173, A:N.173, A:Q.472 Salt bridges: B:K.381, B:K.381, B:K.381, A:R.163, A:R.163, A:R.163, A:R.475 Water bridges: A:D.164, A:I.171, A:Y.476 pi-Stacking: A:F.373 ATP.7: 13 residues within 4Å: Chain A: K.381, R.475, Y.476 Chain B: R.163, D.164, T.166, N.173, F.373, Q.472, R.475 Ligands: ATP.2, MG.4, MG.9 18 PLIP interactions: 13 interactions with chain B, 5 interactions with chain A Hydrogen bonds: B:R.163, B:R.163, B:N.173, B:N.173, B:Q.472, A:R.475, A:Y.476 Water bridges: B:D.164, B:I.171, B:Y.476 Salt bridges: B:R.163, B:R.163, B:R.163, B:R.475, A:K.381, A:K.381, A:K.381 pi-Stacking: B:F.373

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 9 residues within 4Å: Chain A: Q.299, F.302, D.303, I.305, L.340, Q.341, H.342, G.343, I.344 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.341, A:G.343 GOL.8: 9 residues within 4Å: Chain B: Q.299, F.302, D.303, I.305, L.340, Q.341, H.342, G.343, I.344 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.341, B:H.342, B:G.343

4 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 4 residues within 4Å: Chain B: Y.476 Ligands: ATP.2, ATP.7, MG.9 No protein-ligand interaction detected (PLIP) MG.5: 4 residues within 4Å: Chain A: N.71, D.73, D.370 Ligands: U5P.1 5 PLIP interactions: 2 interactions with chain A, 1 Ligand-Ligand interactions, 2 Ligand-Water interactions Metal complexes: A:D.73, A:D.370, U5P.1, H2O.6, H2O.6 MG.9: 4 residues within 4Å: Chain A: Y.476 Ligands: ATP.2, MG.4, ATP.7 No protein-ligand interaction detected (PLIP) MG.10: 4 residues within 4Å: Chain B: N.71, D.73, D.370 Ligands: U5P.6 5 PLIP interactions: 2 interactions with chain B, 1 Ligand-Ligand interactions, 2 Ligand-Water interactions Metal complexes: B:D.73, B:D.370, U5P.6, H2O.13, H2O.13

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wallden, K. et al., Structural Basis for the Allosteric Regulation and Substrate Recognition of Human Cytosolic 5'-Nucleotidase II. J.Mol.Biol. (2011)

Release Date

2011-03-16

Peptides

CYTOSOLIC PURINE 5'-NUCLEOTIDASE: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

CYTOSOLIC PURINE 5'-NUCLEOTIDASE

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