SMTL ID : 2xcv.1

Crystal structure of the D52N variant of cytosolic 5'-nucleotidase II in complex with inosine monophosphate and 2,3-bisphosphoglycerate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-tetramer

Ligands

4 x DG2: (2R)-2,3-diphosphoglyceric acid(Non-covalent)

DG2.1: 8 residues within 4Å: Chain A: R.162, K.380, Y.475 Chain C: R.162, L.376, K.380, Y.475 Ligands: DG2.9 10 PLIP interactions: 6 interactions with chain A, 4 interactions with chain C Hydrogen bonds: A:Y.475, A:Y.475 Water bridges: A:R.474, C:R.162 Salt bridges: A:R.162, A:K.380, A:K.380, C:R.162, C:K.380, C:K.380 DG2.5: 8 residues within 4Å: Chain B: R.162, K.380, Y.475 Chain D: R.162, L.376, K.380, Y.475 Ligands: DG2.13 10 PLIP interactions: 5 interactions with chain B, 5 interactions with chain D Hydrogen bonds: B:Y.475, D:Y.475 Water bridges: B:R.474, D:R.162 Salt bridges: B:R.162, B:K.380, B:K.380, D:R.162, D:K.380, D:K.380 DG2.9: 8 residues within 4Å: Chain A: R.162, L.376, K.380, Y.475 Chain C: R.162, K.380, Y.475 Ligands: DG2.1 10 PLIP interactions: 5 interactions with chain A, 5 interactions with chain C Hydrogen bonds: A:Y.475, C:Y.475 Water bridges: A:R.162, C:R.474 Salt bridges: A:R.162, A:K.380, A:K.380, C:R.162, C:K.380, C:K.380 DG2.13: 8 residues within 4Å: Chain B: R.162, L.376, K.380, Y.475 Chain D: R.162, K.380, Y.475 Ligands: DG2.5 10 PLIP interactions: 4 interactions with chain B, 6 interactions with chain D Water bridges: B:R.162, D:R.474 Salt bridges: B:R.162, B:K.380, B:K.380, D:R.162, D:K.380, D:K.380 Hydrogen bonds: D:Y.475, D:Y.475

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 9 residues within 4Å: Chain A: F.301, D.302, L.303, I.304, Q.340, H.341, G.342, I.343, Y.345 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:I.304, A:G.342 Water bridges: A:Q.298, A:F.301, A:G.342 GOL.6: 9 residues within 4Å: Chain B: F.301, D.302, L.303, I.304, Q.340, H.341, G.342, I.343, Y.345 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:I.304, B:G.342 Water bridges: B:Q.298, B:F.301, B:G.342 GOL.10: 9 residues within 4Å: Chain C: F.301, D.302, L.303, I.304, Q.340, H.341, G.342, I.343, Y.345 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:I.304, C:G.342 Water bridges: C:Q.298, C:F.301, C:G.342 GOL.14: 9 residues within 4Å: Chain D: F.301, D.302, L.303, I.304, Q.340, H.341, G.342, I.343, Y.345 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:I.304, D:G.342 Water bridges: D:Q.298, D:F.301, D:G.342

4 x IMP: INOSINIC ACID(Non-covalent)

IMP.3: 15 residues within 4Å: Chain A: N.70, M.71, D.72, F.175, R.220, V.223, D.224, H.227, Y.228, K.233, T.267, N.268, S.269, K.310 Ligands: MG.4 20 PLIP interactions: 20 interactions with chain A Hydrogen bonds: A:N.70, A:N.70, A:M.71, A:D.72, A:D.72, A:R.220, A:R.220, A:D.224, A:K.233, A:K.233, A:N.268, A:S.269 Water bridges: A:N.176, A:N.268, A:K.310, A:K.310 Salt bridges: A:K.310 pi-Stacking: A:F.175, A:H.227, A:H.227 IMP.7: 15 residues within 4Å: Chain B: N.70, M.71, D.72, F.175, R.220, V.223, D.224, H.227, Y.228, K.233, T.267, N.268, S.269, K.310 Ligands: MG.8 21 PLIP interactions: 21 interactions with chain B Hydrogen bonds: B:N.70, B:N.70, B:M.71, B:D.72, B:R.220, B:R.220, B:D.224, B:D.224, B:K.233, B:K.233, B:T.267, B:N.268, B:S.269 Water bridges: B:N.176, B:N.268, B:K.310, B:K.310 Salt bridges: B:K.310 pi-Stacking: B:F.175, B:H.227, B:H.227 IMP.11: 15 residues within 4Å: Chain C: N.70, M.71, D.72, F.175, R.220, V.223, D.224, H.227, Y.228, K.233, T.267, N.268, S.269, K.310 Ligands: MG.12 21 PLIP interactions: 21 interactions with chain C Hydrogen bonds: C:N.70, C:N.70, C:M.71, C:D.72, C:R.220, C:R.220, C:D.224, C:D.224, C:K.233, C:K.233, C:T.267, C:N.268, C:S.269 Water bridges: C:N.176, C:N.268, C:K.310, C:K.310 Salt bridges: C:K.310 pi-Stacking: C:F.175, C:H.227, C:H.227 IMP.15: 15 residues within 4Å: Chain D: N.70, M.71, D.72, F.175, R.220, V.223, D.224, H.227, Y.228, K.233, T.267, N.268, S.269, K.310 Ligands: MG.16 21 PLIP interactions: 21 interactions with chain D Hydrogen bonds: D:N.70, D:N.70, D:N.70, D:M.71, D:D.72, D:D.72, D:R.220, D:R.220, D:D.224, D:K.233, D:K.233, D:N.268, D:S.269 Water bridges: D:N.176, D:N.268, D:K.310, D:K.310 Salt bridges: D:K.310 pi-Stacking: D:F.175, D:H.227, D:H.227

4 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 4 residues within 4Å: Chain A: N.70, D.72, D.369 Ligands: IMP.3 5 PLIP interactions: 2 interactions with chain A, 1 Ligand-Ligand interactions, 2 Ligand-Water interactions Metal complexes: A:D.72, A:D.369, IMP.3, H2O.9, H2O.9 MG.8: 4 residues within 4Å: Chain B: N.70, D.72, D.369 Ligands: IMP.7 5 PLIP interactions: 2 interactions with chain B, 1 Ligand-Ligand interactions, 2 Ligand-Water interactions Metal complexes: B:D.72, B:D.369, IMP.7, H2O.19, H2O.19 MG.12: 4 residues within 4Å: Chain C: N.70, D.72, D.369 Ligands: IMP.11 5 PLIP interactions: 2 interactions with chain C, 1 Ligand-Ligand interactions, 2 Ligand-Water interactions Metal complexes: C:D.72, C:D.369, IMP.11, H2O.29, H2O.29 MG.16: 4 residues within 4Å: Chain D: N.70, D.72, D.369 Ligands: IMP.15 4 PLIP interactions: 2 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:D.72, D:D.369, H2O.39, H2O.39

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: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

CYTOSOLIC PURINE 5'-NUCLEOTIDASE

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