SMTL ID : 6ddz.1

Crystal structure of the double mutant (D52N/R238W) of NT5C2-537X in the active state, Northeast Structural Genomics Target

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.97 Å

Oligo State

homo-tetramer

Ligands

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

ATP.1: 13 residues within 4Å: Chain A: R.162, D.163, I.170, N.172, F.372, Q.471, R.474 Chain C: K.380, R.474, Y.475 Ligands: MG.2, ATP.13, MG.14 22 PLIP interactions: 14 interactions with chain A, 8 interactions with chain C Hydrogen bonds: A:R.162, A:N.172, A:N.172, A:Q.471, C:R.474, C:Y.475 Water bridges: A:A.132, A:I.170, A:K.380, A:R.474, A:Y.475, C:K.380, C:K.380, C:Y.475 Salt bridges: A:R.162, A:R.162, A:R.162, A:R.474, C:K.380, C:K.380, C:K.380 pi-Stacking: A:F.372 ATP.7: 13 residues within 4Å: Chain B: R.162, D.163, I.170, N.172, F.372, Q.471, R.474 Chain D: K.380, R.474, Y.475 Ligands: MG.8, ATP.19, MG.20 22 PLIP interactions: 14 interactions with chain B, 8 interactions with chain D Hydrogen bonds: B:R.162, B:N.172, B:N.172, B:Q.471, D:R.474, D:Y.475 Water bridges: B:A.132, B:I.170, B:K.380, B:R.474, B:Y.475, D:K.380, D:K.380, 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.13: 13 residues within 4Å: Chain A: K.380, R.474, Y.475 Chain C: R.162, D.163, I.170, N.172, F.372, Q.471, R.474 Ligands: ATP.1, MG.2, MG.14 24 PLIP interactions: 8 interactions with chain A, 16 interactions with chain C Hydrogen bonds: A:R.474, A:Y.475, A:Y.475, C:R.162, C:N.172, C:N.172, C:Q.471 Water bridges: A:K.380, A:K.380, C:A.132, C:I.170, C:K.380, C:R.474, C:Y.475, C:Y.475, C:Y.475 Salt bridges: A:K.380, A:K.380, A:K.380, C:R.162, C:R.162, C:R.162, C:R.474 pi-Stacking: C:F.372 ATP.19: 13 residues within 4Å: Chain B: K.380, R.474, Y.475 Chain D: R.162, D.163, I.170, N.172, F.372, Q.471, R.474 Ligands: ATP.7, MG.8, MG.20 24 PLIP interactions: 8 interactions with chain B, 16 interactions with chain D Hydrogen bonds: B:R.474, B:Y.475, B:Y.475, D:R.162, D:N.172, D:N.172, D:Q.471 Water bridges: B:K.380, B:K.380, D:A.132, D:I.170, 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

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

MG.2: 3 residues within 4Å: Ligands: ATP.1, ATP.13, MG.14 No protein-ligand interaction detected (PLIP) MG.4: 4 residues within 4Å: Chain A: N.70, D.72, D.369 Ligands: PO4.3 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.72, A:D.369, H2O.2, H2O.6 MG.8: 3 residues within 4Å: Ligands: ATP.7, ATP.19, MG.20 No protein-ligand interaction detected (PLIP) MG.10: 4 residues within 4Å: Chain B: N.70, D.72, D.369 Ligands: PO4.9 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.72, B:D.369, H2O.15, H2O.19 MG.14: 3 residues within 4Å: Ligands: ATP.1, MG.2, ATP.13 No protein-ligand interaction detected (PLIP) MG.16: 4 residues within 4Å: Chain C: N.70, D.72, D.369 Ligands: PO4.15 4 PLIP interactions: 2 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.72, C:D.369, H2O.28, H2O.32 MG.20: 3 residues within 4Å: Ligands: ATP.7, MG.8, ATP.19 No protein-ligand interaction detected (PLIP) MG.22: 4 residues within 4Å: Chain D: N.70, D.72, D.369 Ligands: PO4.21 4 PLIP interactions: 2 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:D.72, D:D.369, H2O.41, H2O.45

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

PO4.3: 8 residues within 4Å: Chain A: N.70, M.71, D.72, T.267, N.268, S.269, K.310 Ligands: MG.4 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:M.71, A:D.72, A:T.267, A:T.267, A:T.267, A:N.268, A:S.269 Water bridges: A:K.310 Salt bridges: A:K.310 PO4.9: 8 residues within 4Å: Chain B: N.70, M.71, D.72, T.267, N.268, S.269, K.310 Ligands: MG.10 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:M.71, B:D.72, B:T.267, B:T.267, B:T.267, B:N.268, B:S.269 Water bridges: B:K.310 Salt bridges: B:K.310 PO4.15: 8 residues within 4Å: Chain C: N.70, M.71, D.72, T.267, N.268, S.269, K.310 Ligands: MG.16 11 PLIP interactions: 11 interactions with chain C Hydrogen bonds: C:M.71, C:D.72, C:D.72, C:T.267, C:T.267, C:N.268, C:S.269 Water bridges: C:D.72, C:K.310, C:K.310 Salt bridges: C:K.310 PO4.21: 8 residues within 4Å: Chain D: N.70, M.71, D.72, T.267, N.268, S.269, K.310 Ligands: MG.22 9 PLIP interactions: 9 interactions with chain D Hydrogen bonds: D:M.71, D:D.72, D:D.72, D:T.267, D:T.267, D:N.268, D:S.269 Water bridges: D:K.310 Salt bridges: D:K.310

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 6 residues within 4Å: Chain A: D.270, Y.271, V.306, D.307, G.328, L.330 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.271, A:L.330 Water bridges: A:K.272 GOL.6: 8 residues within 4Å: Chain A: F.301, D.302, I.304, L.339, Q.340, H.341, G.342, I.343 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.341, A:G.342 Water bridges: A:I.304 GOL.11: 6 residues within 4Å: Chain B: D.270, Y.271, V.306, D.307, G.328, L.330 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Y.271, B:L.330 Water bridges: B:K.272 GOL.12: 8 residues within 4Å: Chain B: F.301, D.302, I.304, L.339, Q.340, H.341, G.342, I.343 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:H.341, B:G.342 Water bridges: B:I.304 GOL.17: 6 residues within 4Å: Chain C: D.270, Y.271, V.306, D.307, G.328, L.330 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:Y.271, C:L.330 Water bridges: C:K.272 GOL.18: 8 residues within 4Å: Chain C: F.301, D.302, I.304, L.339, Q.340, H.341, G.342, I.343 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:H.341, C:G.342 Water bridges: C:I.304 GOL.23: 6 residues within 4Å: Chain D: D.270, Y.271, V.306, D.307, G.328, L.330 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:Y.271, D:L.330 Water bridges: D:K.272 GOL.24: 8 residues within 4Å: Chain D: F.301, D.302, I.304, L.339, Q.340, H.341, G.342, I.343 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:H.341, D:G.342 Water bridges: D:I.304

Links

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Citation

Dieck, C.L. et al., Structure and Mechanisms of NT5C2 Mutations Driving Thiopurine Resistance in Relapsed Lymphoblastic Leukemia. Cancer Cell (2018)

Release Date

2018-07-04

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