SMTL ID : 2xjb.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-dimer

Ligands

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 8 residues within 4Å: Chain A: S.111, T.112, P.114, T.115, E.392, E.396, Y.452, G.456 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.111, A:G.456 Water bridges: A:G.456 GOL.4: 8 residues within 4Å: Chain A: F.301, D.302, I.304, L.339, Q.340, H.341, G.342, I.343 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.340, A:H.341, A:G.342 Water bridges: A:I.304 GOL.5: 7 residues within 4Å: Chain A: D.270, Y.271, K.272, V.306, D.307, G.328, L.330 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.270, A:Y.271, A:K.272 GOL.8: 8 residues within 4Å: Chain B: S.111, T.112, P.114, T.115, E.392, E.396, Y.452, G.456 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.111, B:E.396, B:G.456 Water bridges: B:G.456 GOL.11: 8 residues within 4Å: Chain B: F.301, D.302, I.304, L.339, Q.340, H.341, G.342, I.343 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Q.340, B:H.341, B:G.342 Water bridges: B:I.304 GOL.12: 7 residues within 4Å: Chain B: D.270, Y.271, K.272, V.306, D.307, G.328, L.330 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:D.270, B:D.270, B:Y.271, B:K.272

2 x DTP: 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE(Non-covalent)

DTP.2: 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.7, DTP.9, MG.14 19 PLIP interactions: 14 interactions with chain A, 5 interactions with chain B Hydrogen bonds: A:R.162, A:N.172, A:N.172, A:Q.471, B:R.474, B:Y.475 Water bridges: A:I.170, A:R.474, A:R.474, A:Y.475, A:Y.475 Salt bridges: A:R.162, A:R.162, A:R.162, A:R.474, B:K.380, B:K.380, B:K.380 pi-Stacking: A:F.372 DTP.9: 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: DTP.2, MG.7, MG.14 21 PLIP interactions: 15 interactions with chain B, 6 interactions with chain A Hydrogen bonds: B:R.162, B:N.172, B:N.172, B:Q.471, A:R.474 Water bridges: B:R.162, B:R.162, B:I.170, B:R.474, B:R.474, B:Y.475, A:Y.475, A: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

2 x DG: 2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE(Non-covalent)

DG.3: 14 residues within 4Å: Chain A: N.70, M.71, D.72, F.175, R.220, V.223, D.224, H.227, K.233, T.267, N.268, S.269, K.310 Ligands: MG.6 45 PLIP interactions: 23 interactions with chain B, 22 interactions with chain A Hydrophobic interactions: B:F.175, A:F.175 Hydrogen bonds: B:N.70, B:N.70, B:N.70, B:M.71, B:D.72, B:R.220, B:R.220, B:D.224, B:K.233, B:T.267, B:N.268, B:S.269, A:N.70, A:N.70, A:N.70, A:M.71, A:D.72, A:D.72, A:R.220, A:R.220, A:K.233, A:N.268, A:S.269 Water bridges: B:N.176, B:K.310, B:K.310, B:K.310, B:K.310, A:N.176, A:K.310, A:K.310, A:K.310, A:K.310 Salt bridges: B:D.224, B:K.310, A:D.224, A:K.310 pi-Stacking: B:F.175, B:H.227, B:H.227, A:F.175, A:H.227, A:H.227 DG.10: 14 residues within 4Å: Chain B: N.70, M.71, D.72, F.175, R.220, V.223, D.224, H.227, K.233, T.267, N.268, S.269, K.310 Ligands: MG.13 Protein-ligand interaction information (PLIP) not available

4 x MG: MAGNESIUM ION(Non-covalent)(Non-functional Binders)

MG.6: 4 residues within 4Å: Chain A: N.70, D.72, D.369 Ligands: DG.3 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.72, A:D.369, H2O.9, H2O.9 MG.7: 3 residues within 4Å: Ligands: DTP.2, DTP.9, MG.14 No protein-ligand interaction detected (PLIP) MG.13: 4 residues within 4Å: Chain B: N.70, D.72, D.369 Ligands: DG.10 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.72, B:D.369, H2O.19, H2O.19 MG.14: 3 residues within 4Å: Ligands: DTP.2, MG.7, DTP.9 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

2011-03-16

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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