SMTL ID : 6ddb.1

Crystal structure of the double mutant (D52N/R367Q) of NT5C2-537X in the basal state, Northeast Structural Genomics Consortium Target

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

homo-tetramer

Ligands

4 x MN: MANGANESE (II) ION(Non-covalent)

MN.1: 4 residues within 4Å: Chain A: N.70, D.72, D.369 Ligands: PO4.2 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.72, A:D.369, H2O.3 MN.4: 4 residues within 4Å: Chain B: N.70, D.72, D.369 Ligands: PO4.5 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:D.72, B:D.369 MN.7: 4 residues within 4Å: Chain C: N.70, D.72, D.369 Ligands: PO4.8 3 PLIP interactions: 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.72, C:D.369, H2O.10 MN.10: 4 residues within 4Å: Chain D: N.70, D.72, D.369 Ligands: PO4.11 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:D.72, D:D.369

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

PO4.2: 8 residues within 4Å: Chain A: N.70, M.71, D.72, T.267, N.268, S.269, K.310 Ligands: MN.1 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:N.70, A:N.70, A:M.71, A:D.72, A:D.72, A:D.72, A:D.72, A:T.267, A:N.268, A:S.269 Salt bridges: A:K.310 PO4.3: 6 residues within 4Å: Chain A: R.52, V.53, V.55, Y.489, Y.493, F.495 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.493 Water bridges: A:R.52 Salt bridges: A:R.52 PO4.5: 8 residues within 4Å: Chain B: N.70, M.71, D.72, T.267, N.268, S.269, K.310 Ligands: MN.4 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:M.71, B:D.72, B:T.267, B:T.267, B:N.268, B:S.269 Salt bridges: B:K.310 PO4.6: 6 residues within 4Å: Chain B: R.52, V.53, V.55, Y.489, Y.493, F.495 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Y.489, B:Y.489 Water bridges: B:Y.493 Salt bridges: B:R.52 PO4.8: 8 residues within 4Å: Chain C: N.70, M.71, D.72, T.267, N.268, S.269, K.310 Ligands: MN.7 8 PLIP interactions: 8 interactions with chain C Hydrogen bonds: C:N.70, C:M.71, C:D.72, C:D.72, C:D.72, C:N.268, C:S.269 Salt bridges: C:K.310 PO4.9: 6 residues within 4Å: Chain C: R.52, V.53, V.55, Y.489, Y.493, F.495 3 PLIP interactions: 1 interactions with chain D, 2 interactions with chain C Water bridges: D:T.507 Hydrogen bonds: C:Y.489 Salt bridges: C:R.52 PO4.11: 8 residues within 4Å: Chain D: N.70, M.71, D.72, T.267, N.268, S.269, K.310 Ligands: MN.10 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:T.267, D:N.268, D:S.269 Salt bridges: D:K.310 PO4.12: 6 residues within 4Å: Chain D: R.52, V.53, V.55, Y.489, Y.493, F.495 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:Y.489, D:Y.493 Salt bridges: D:R.52

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
B

C
A

D
B

Cytosolic purine 5'-nucleotidase

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