SMTL ID : 6de3.1

Crystal structure of the double mutant (R39Q/D52N) of the full-length NT5C2 in the active state

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.06 Å

Oligo State

homo-tetramer

Ligands

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

PO4.1: 8 residues within 4Å: Chain A: N.70, M.71, D.72, T.267, N.268, S.269, K.310, D.369 10 PLIP interactions: 10 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:N.268, A:S.269 Salt bridges: A:K.310 PO4.4: 8 residues within 4Å: Chain B: N.70, M.71, D.72, T.267, N.268, S.269, K.310, D.369 10 PLIP interactions: 10 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:N.268, B:S.269 Salt bridges: B:K.310 PO4.7: 8 residues within 4Å: Chain C: N.70, M.71, D.72, T.267, N.268, S.269, K.310, D.369 10 PLIP interactions: 10 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:N.268, C:S.269 Salt bridges: C:K.310 PO4.10: 8 residues within 4Å: Chain D: N.70, M.71, D.72, T.267, N.268, S.269, K.310, D.369 10 PLIP interactions: 10 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:N.268, D:S.269 Salt bridges: D:K.310

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

ATP.2: 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.3, ATP.8, MG.9 14 PLIP interactions: 10 interactions with chain A, 4 interactions with chain C Hydrogen bonds: A:R.162, A:N.172, A:N.172, A:Q.471, C:R.474 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, A:F.372 ATP.5: 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.6, ATP.11, MG.12 14 PLIP interactions: 10 interactions with chain B, 4 interactions with chain D Hydrogen bonds: B:R.162, B:N.172, B:N.172, B:Q.471, D:R.474 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, B:F.372 ATP.8: 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.2, MG.3, MG.9 15 PLIP interactions: 10 interactions with chain C, 5 interactions with chain A Hydrogen bonds: C:R.162, C:N.172, C:N.172, C:Q.471, A:R.474, 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, C:F.372 ATP.11: 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.5, MG.6, MG.12 15 PLIP interactions: 10 interactions with chain D, 5 interactions with chain B Hydrogen bonds: D:R.162, D:N.172, D:N.172, D:Q.471, B:R.474, B:Y.475 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, D:F.372

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

MG.3: 3 residues within 4Å: Ligands: ATP.2, ATP.8, MG.9 No protein-ligand interaction detected (PLIP) MG.6: 3 residues within 4Å: Ligands: ATP.5, ATP.11, MG.12 No protein-ligand interaction detected (PLIP) MG.9: 3 residues within 4Å: Ligands: ATP.2, MG.3, ATP.8 No protein-ligand interaction detected (PLIP) MG.12: 3 residues within 4Å: Ligands: ATP.5, MG.6, ATP.11 No protein-ligand interaction detected (PLIP)

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

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