SMTL ID : 2xcw.1

Crystal structure of the D52N variant of cytosolic 5'-nucleotidase II in complex with inosine monophosphate and ATP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-tetramer

Ligands

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

ATP.1: 15 residues within 4Å: Chain A: R.162, D.163, T.165, I.170, N.172, F.372, Q.471, R.474 Chain C: K.380, R.474, Y.475 Ligands: GOL.7, MG.9, ATP.21, MG.29 30 PLIP interactions: 10 interactions with chain C, 20 interactions with chain A Hydrogen bonds: C:R.474, C:Y.475, A:R.162, A:N.172, A:N.172, A:Q.471 Water bridges: C:K.380, C:K.380, C:K.380, C:K.380, C:K.380, A:D.163, A:D.163, A:K.377, A:K.380, A:K.380, A:K.380, A:K.380, A:R.474, A:Y.475, A:Y.475, A:Y.475 Salt bridges: C:K.380, C:K.380, C:K.380, A:R.162, A:R.162, A:R.162, A:R.474 pi-Stacking: A:F.372 ATP.11: 15 residues within 4Å: Chain B: R.162, D.163, T.165, I.170, N.172, F.372, Q.471, R.474 Chain D: K.380, R.474, Y.475 Ligands: GOL.17, MG.19, ATP.31, MG.39 29 PLIP interactions: 20 interactions with chain B, 9 interactions with chain D Hydrogen bonds: B:R.162, B:N.172, B:N.172, B:Q.471, D:R.474 Water bridges: B:D.163, B:D.163, B:K.377, B:K.380, B:K.380, B:K.380, B:K.380, B:R.474, B:R.474, B:R.474, B:Y.475, D:K.380, D:K.380, D:K.380, D:Y.475, D:Y.475 Salt bridges: B:R.162, B:R.162, B:R.162, B:R.474, D:K.380, D:K.380, D:K.380 pi-Stacking: B:F.372 ATP.21: 15 residues within 4Å: Chain A: K.380, R.474, Y.475 Chain C: R.162, D.163, T.165, I.170, N.172, F.372, Q.471, R.474 Ligands: ATP.1, MG.9, GOL.27, MG.29 29 PLIP interactions: 20 interactions with chain C, 9 interactions with chain A Hydrogen bonds: C:R.162, C:N.172, C:N.172, C:Q.471, A:R.474 Water bridges: C:D.163, C:D.163, C:K.377, C:K.380, C:K.380, C:K.380, C:K.380, C:R.474, C:R.474, C:R.474, C:Y.475, A:K.380, A:K.380, A:K.380, A:Y.475, A:Y.475 Salt bridges: C:R.162, C:R.162, C:R.162, C:R.474, A:K.380, A:K.380, A:K.380 pi-Stacking: C:F.372 ATP.31: 15 residues within 4Å: Chain B: K.380, R.474, Y.475 Chain D: R.162, D.163, T.165, I.170, N.172, F.372, Q.471, R.474 Ligands: ATP.11, MG.19, GOL.37, MG.39 30 PLIP interactions: 10 interactions with chain B, 20 interactions with chain D Hydrogen bonds: B:R.474, B:Y.475, D:R.162, D:N.172, D:N.172, D:Q.471 Water bridges: B:K.380, B:K.380, B:K.380, B:K.380, B:K.380, D:D.163, D:D.163, D:K.377, D:K.380, D:K.380, D:K.380, D:K.380, D:R.474, D:Y.475, D:Y.475, D:Y.475 Salt bridges: B:K.380, B:K.380, B:K.380, D:R.162, D:R.162, D:R.162, D:R.474 pi-Stacking: D:F.372

4 x IMP: INOSINIC ACID(Non-covalent)

IMP.2: 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.10 22 PLIP interactions: 22 interactions with chain A Hydrogen bonds: A:N.70, A:N.70, A:M.71, A:D.72, A:R.220, A:R.220, A:D.224, A:K.233, A:K.233, A:N.268, A:S.269, A:S.269 Water bridges: A:N.176, A:Y.228, A:N.268, 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.12: 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.20 24 PLIP interactions: 24 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, B:S.269 Water bridges: B:Y.83, B:N.176, B:N.268, 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.22: 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.30 24 PLIP interactions: 24 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, C:S.269 Water bridges: C:Y.83, C:N.176, C:N.268, 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.32: 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.40 23 PLIP interactions: 23 interactions with chain D Hydrogen bonds: D:N.70, D:N.70, D:N.70, D:M.71, D:D.72, D:R.220, D:R.220, D:D.224, D:K.233, D:K.233, D:N.268, D:S.269, D:S.269 Water bridges: D:N.176, D:Y.228, D:N.268, 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

24 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 8 residues within 4Å: Chain A: F.301, D.302, I.304, L.339, Q.340, H.341, G.342, I.343 Ligand excluded by PLIP GOL.4: 5 residues within 4Å: Chain A: Y.169, F.216, Q.217, R.220, D.224 Ligand excluded by PLIP GOL.5: 6 residues within 4Å: Chain A: P.114, T.115, E.392, E.396, Y.452, L.458 Ligand excluded by PLIP GOL.6: 5 residues within 4Å: Chain A: D.275, T.279, P.296, W.297, Q.298 Ligand excluded by PLIP GOL.7: 7 residues within 4Å: Chain A: Y.169, I.170, L.171, N.172, N.176, H.370 Ligands: ATP.1 Ligand excluded by PLIP GOL.8: 7 residues within 4Å: Chain A: D.270, Y.271, V.306, D.307, G.328, K.329, L.330 Ligand excluded by PLIP GOL.13: 8 residues within 4Å: Chain B: F.301, D.302, I.304, L.339, Q.340, H.341, G.342, I.343 Ligand excluded by PLIP GOL.14: 5 residues within 4Å: Chain B: Y.169, F.216, Q.217, R.220, D.224 Ligand excluded by PLIP GOL.15: 6 residues within 4Å: Chain B: P.114, T.115, E.392, E.396, Y.452, L.458 Ligand excluded by PLIP GOL.16: 5 residues within 4Å: Chain B: D.275, T.279, P.296, W.297, Q.298 Ligand excluded by PLIP GOL.17: 7 residues within 4Å: Chain B: Y.169, I.170, L.171, N.172, N.176, H.370 Ligands: ATP.11 Ligand excluded by PLIP GOL.18: 7 residues within 4Å: Chain B: D.270, Y.271, V.306, D.307, G.328, K.329, L.330 Ligand excluded by PLIP GOL.23: 8 residues within 4Å: Chain C: F.301, D.302, I.304, L.339, Q.340, H.341, G.342, I.343 Ligand excluded by PLIP GOL.24: 5 residues within 4Å: Chain C: Y.169, F.216, Q.217, R.220, D.224 Ligand excluded by PLIP GOL.25: 6 residues within 4Å: Chain C: P.114, T.115, E.392, E.396, Y.452, L.458 Ligand excluded by PLIP GOL.26: 5 residues within 4Å: Chain C: D.275, T.279, P.296, W.297, Q.298 Ligand excluded by PLIP GOL.27: 7 residues within 4Å: Chain C: Y.169, I.170, L.171, N.172, N.176, H.370 Ligands: ATP.21 Ligand excluded by PLIP GOL.28: 7 residues within 4Å: Chain C: D.270, Y.271, V.306, D.307, G.328, K.329, L.330 Ligand excluded by PLIP GOL.33: 8 residues within 4Å: Chain D: F.301, D.302, I.304, L.339, Q.340, H.341, G.342, I.343 Ligand excluded by PLIP GOL.34: 5 residues within 4Å: Chain D: Y.169, F.216, Q.217, R.220, D.224 Ligand excluded by PLIP GOL.35: 6 residues within 4Å: Chain D: P.114, T.115, E.392, E.396, Y.452, L.458 Ligand excluded by PLIP GOL.36: 5 residues within 4Å: Chain D: D.275, T.279, P.296, W.297, Q.298 Ligand excluded by PLIP GOL.37: 7 residues within 4Å: Chain D: Y.169, I.170, L.171, N.172, N.176, H.370 Ligands: ATP.31 Ligand excluded by PLIP GOL.38: 7 residues within 4Å: Chain D: D.270, Y.271, V.306, D.307, G.328, K.329, L.330 Ligand excluded by PLIP

8 x MG: MAGNESIUM ION(Non-covalent)

MG.9: 4 residues within 4Å: Chain C: K.380 Ligands: ATP.1, ATP.21, MG.29 No protein-ligand interaction detected (PLIP) MG.10: 4 residues within 4Å: Chain A: N.70, D.72, D.369 Ligands: IMP.2 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.72, A:D.369, H2O.13, H2O.13 MG.19: 4 residues within 4Å: Chain D: K.380 Ligands: ATP.11, ATP.31, MG.39 No protein-ligand interaction detected (PLIP) MG.20: 4 residues within 4Å: Chain B: N.70, D.72, D.369 Ligands: IMP.12 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.72, B:D.369, H2O.29, H2O.29 MG.29: 4 residues within 4Å: Chain A: K.380 Ligands: ATP.1, MG.9, ATP.21 No protein-ligand interaction detected (PLIP) MG.30: 4 residues within 4Å: Chain C: N.70, D.72, D.369 Ligands: IMP.22 4 PLIP interactions: 2 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.72, C:D.369, H2O.45, H2O.45 MG.39: 4 residues within 4Å: Chain B: K.380 Ligands: ATP.11, MG.19, ATP.31 No protein-ligand interaction detected (PLIP) MG.40: 4 residues within 4Å: Chain D: N.70, D.72, D.369 Ligands: IMP.32 4 PLIP interactions: 2 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:D.72, D:D.369, H2O.60, H2O.60

Links

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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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