SMTL ID : 2xjd.1

Crystal structure of the D52N variant of cytosolic 5'-nucleotidase II in complex with inorganic phosphate and deoxyadenosine triphosphate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

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

ATP.1: 14 residues within 4Å: Chain A: R.162, D.163, T.165, I.170, N.172, F.372, Q.471, R.474 Chain B: K.380, R.474, Y.475 Ligands: MG.10, ATP.11, MG.20 20 PLIP interactions: 5 interactions with chain B, 15 interactions with chain A Hydrogen bonds: B:R.474, A:R.162, A:N.172, A:N.172, A:Q.471 Water bridges: B:Y.475, A:R.162, A:R.162, A:R.162, A:D.163, A:D.163, A:I.170 Salt bridges: B:K.380, B:K.380, B:K.380, A:R.162, A:R.162, A:R.162, A:R.474 pi-Stacking: A:F.372 ATP.11: 14 residues within 4Å: Chain A: K.380, R.474, Y.475 Chain B: R.162, D.163, T.165, I.170, N.172, F.372, Q.471, R.474 Ligands: ATP.1, MG.10, MG.20 21 PLIP interactions: 16 interactions with chain B, 5 interactions with chain A Hydrogen bonds: B:R.162, B:N.172, B:N.172, B:Q.471, A:R.474, A:Y.475 Water bridges: B:R.162, B:R.162, B:D.163, B:D.163, B:I.170, B:Y.475, B:Y.475 Salt bridges: B:R.162, B:R.162, B:R.162, B:R.474, A:K.380, A:K.380, A:K.380 pi-Stacking: B:F.372

12 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 8 residues within 4Å: Chain A: D.72, F.175, H.227, Y.228, K.233, S.269, Y.273 Ligands: GOL.5 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Y.83, A:Y.228, A:K.233 Water bridges: A:N.268, A:D.270 GOL.3: 8 residues within 4Å: Chain A: F.301, D.302, I.304, L.339, Q.340, H.341, G.342, I.343 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:F.301, A:Q.340, A:G.342 Water bridges: A:I.304, A:G.342 GOL.4: 4 residues within 4Å: Chain A: R.213, F.216, Q.217, R.220 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.213, A:Q.217, A:R.220, A:D.224 Water bridges: A:Y.169, A:D.221 GOL.5: 7 residues within 4Å: Chain A: F.175, R.220, V.223, D.224, H.227, Y.228 Ligands: GOL.2 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.220, A:R.220, A:D.224, A:Y.228, A:Y.228 Water bridges: A:T.173 GOL.6: 6 residues within 4Å: Chain A: P.114, T.115, E.392, E.396, Y.452, L.458 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:P.114, A:E.396, A:Y.452, A:L.458 GOL.7: 5 residues within 4Å: Chain A: D.275, T.279, P.296, W.297, Q.298 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.275, A:Q.298, A:Q.298 Water bridges: A:W.297 GOL.12: 8 residues within 4Å: Chain B: D.72, F.175, H.227, Y.228, K.233, S.269, Y.273 Ligands: GOL.15 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:Y.83, B:Y.83, B:Y.228, B:Y.228, B:K.233 Water bridges: B:N.268, B:D.270 GOL.13: 8 residues within 4Å: Chain B: F.301, D.302, I.304, L.339, Q.340, H.341, G.342, I.343 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:F.301, B:Q.340, B:H.341, B:G.342 Water bridges: B:I.304, B:G.342 GOL.14: 4 residues within 4Å: Chain B: R.213, F.216, Q.217, R.220 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:R.213, B:Q.217, B:R.220, B:D.224 Water bridges: B:D.221 GOL.15: 7 residues within 4Å: Chain B: F.175, R.220, V.223, D.224, H.227, Y.228 Ligands: GOL.12 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.220, B:R.220, B:Y.228 GOL.16: 6 residues within 4Å: Chain B: P.114, T.115, E.392, E.396, Y.452, L.458 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:P.114, B:Y.452, B:L.458 GOL.17: 5 residues within 4Å: Chain B: D.275, T.279, P.296, W.297, Q.298 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:D.275, B:Q.298, B:Q.298 Water bridges: B:Y.271, B:W.297

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

PO4.8: 8 residues within 4Å: Chain A: N.70, M.71, D.72, T.267, N.268, S.269, K.310 Ligands: MG.9 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:N.70, A:M.71, A:D.72, A:T.267, A:N.268, A:S.269 Water bridges: A:K.310, A:K.310, A:K.310 Salt bridges: A:K.310 PO4.18: 8 residues within 4Å: Chain B: N.70, M.71, D.72, T.267, N.268, S.269, K.310 Ligands: MG.19 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:N.70, B:M.71, B:D.72, B:D.72, B:N.268, B:S.269 Water bridges: B:K.310, B:K.310, B:K.310 Salt bridges: B:K.310

4 x MG: MAGNESIUM ION(Non-covalent)

MG.9: 4 residues within 4Å: Chain A: N.70, D.72, D.369 Ligands: PO4.8 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.72, A:D.369, H2O.15, H2O.15 MG.10: 4 residues within 4Å: Chain A: Y.475 Ligands: ATP.1, ATP.11, MG.20 No protein-ligand interaction detected (PLIP) MG.19: 4 residues within 4Å: Chain B: N.70, D.72, D.369 Ligands: PO4.18 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.72, B:D.369, H2O.32, H2O.32 MG.20: 4 residues within 4Å: Chain B: Y.475 Ligands: ATP.1, MG.10, ATP.11 No protein-ligand interaction detected (PLIP)

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

2011-04-27

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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