SMTL ID : 6de2.1

Crystal structure of the double mutant (D52N/L375F) of the full-length NT5C2 in the active state

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-tetramer

Ligands

4 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 C: K.380, R.474, Y.475 Ligands: MG.2, ATP.13, MG.14 21 PLIP interactions: 14 interactions with chain A, 7 interactions with chain C Hydrogen bonds: A:R.162, A:N.172, A:N.172, A:Q.471, C:R.474 Water bridges: A:I.170, A:R.474, A:R.474, A:R.474, A:R.474, C:K.380, C:Y.475, 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: 14 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: MG.8, ATP.19, MG.20 21 PLIP interactions: 14 interactions with chain B, 7 interactions with chain D Hydrogen bonds: B:R.162, B:N.172, B:N.172, B:Q.471, D:R.474 Water bridges: B:I.170, B:R.474, B:R.474, B:R.474, B:R.474, 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.13: 14 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.2, MG.14 20 PLIP interactions: 14 interactions with chain C, 6 interactions with chain A Hydrogen bonds: C:R.162, C:N.172, C:N.172, C:Q.471, A:R.474, A:Y.475 Water bridges: C:I.170, C:R.474, C:Y.475, C:Y.475, C:Y.475, A:K.380 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.19: 14 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.7, MG.8, MG.20 20 PLIP interactions: 14 interactions with chain D, 6 interactions with chain B Hydrogen bonds: D:R.162, D:N.172, D:N.172, D:Q.471, B:R.474, B:Y.475 Water bridges: D:I.170, D:R.474, D:Y.475, D:Y.475, D:Y.475, B:K.380 Salt bridges: D:R.162, D:R.162, D:R.162, D:R.474, B:K.380, B:K.380, B:K.380 pi-Stacking: D:F.372

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

MG.2: 3 residues within 4Å: Ligands: ATP.1, ATP.13, MG.14 No protein-ligand interaction detected (PLIP) MG.8: 3 residues within 4Å: Ligands: ATP.7, ATP.19, MG.20 No protein-ligand interaction detected (PLIP) MG.14: 3 residues within 4Å: Ligands: ATP.1, MG.2, ATP.13 No protein-ligand interaction detected (PLIP) MG.20: 3 residues within 4Å: Ligands: ATP.7, MG.8, ATP.19 No protein-ligand interaction detected (PLIP)

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, D.369 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:N.70, 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, A:D.369 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, D.369 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:N.70, 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, B:D.369 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, D.369 11 PLIP interactions: 11 interactions with chain C Hydrogen bonds: C:N.70, C:M.71, C:D.72, C:D.72, C:T.267, C:T.267, C:N.268, C:S.269 Water bridges: C:K.310, C:D.369 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, D.369 11 PLIP interactions: 11 interactions with chain D Hydrogen bonds: D:N.70, 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, D:D.369 Salt bridges: D:K.310

12 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.4: 6 residues within 4Å: Chain A: D.270, Y.271, V.306, D.307, G.328, L.330 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.271 Water bridges: A:D.270 EDO.5: 5 residues within 4Å: Chain A: F.175, R.220, V.223, D.224, H.227 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.220, A:R.220, A:D.224, A:D.224 Water bridges: A:T.173, A:N.176 EDO.6: 8 residues within 4Å: Chain A: D.72, Y.78, Y.83, F.175, H.227, K.233, S.269, Y.273 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.72, A:H.227, A:K.233 Water bridges: A:K.233, A:K.233 EDO.10: 6 residues within 4Å: Chain B: D.270, Y.271, V.306, D.307, G.328, L.330 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Y.271 Water bridges: B:D.270 EDO.11: 5 residues within 4Å: Chain B: F.175, R.220, V.223, D.224, H.227 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:R.220, B:R.220, B:D.224, B:D.224 Water bridges: B:T.173, B:N.176 EDO.12: 8 residues within 4Å: Chain B: D.72, Y.78, Y.83, F.175, H.227, K.233, S.269, Y.273 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:D.72, B:H.227, B:K.233 Water bridges: B:K.233, B:K.233 EDO.16: 6 residues within 4Å: Chain C: D.270, Y.271, V.306, D.307, G.328, L.330 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:Y.271 Water bridges: C:K.272 EDO.17: 5 residues within 4Å: Chain C: F.175, R.220, V.223, D.224, H.227 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:R.220, C:R.220, C:D.224 Water bridges: C:T.173, C:N.176 EDO.18: 8 residues within 4Å: Chain C: D.72, Y.78, Y.83, F.175, H.227, K.233, S.269, Y.273 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:D.72, C:K.233 Water bridges: C:D.72, C:K.233, C:K.233 EDO.22: 6 residues within 4Å: Chain D: D.270, Y.271, V.306, D.307, G.328, L.330 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:Y.271 Water bridges: D:K.272 EDO.23: 5 residues within 4Å: Chain D: F.175, R.220, V.223, D.224, H.227 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:R.220, D:R.220, D:D.224 Water bridges: D:T.173, D:N.176 EDO.24: 8 residues within 4Å: Chain D: D.72, Y.78, Y.83, F.175, H.227, K.233, S.269, Y.273 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:D.72, D:K.233 Water bridges: D:D.72, D:K.233, D:K.233

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

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