SMTL ID : 6ddq.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.31 Å

Oligo State

homo-tetramer

Ligands

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

PO4.1: 6 residues within 4Å: Chain A: R.52, V.53, V.55, Y.489, Y.493, F.495 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:Y.489 Water bridges: A:K.44, A:K.44, A:R.46, A:R.52, A:Y.493, A:Y.493, A:Y.493, A:Y.493, A:L.494, A:R.496 Salt bridges: A:R.52 PO4.2: 7 residues within 4Å: Chain A: N.70, M.71, D.72, T.267, N.268, S.269, K.310 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:N.70, A:N.70, A:M.71, A:D.72, A:D.72, A:T.267, A:T.267, A:N.268, A:S.269 Salt bridges: A:K.310 PO4.4: 6 residues within 4Å: Chain B: R.52, V.53, V.55, Y.489, Y.493, F.495 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:V.53, B:V.53, B:Y.493 Water bridges: B:R.47, B:R.47, B:Y.493, B:Y.493, B:Y.493 Salt bridges: B:R.52 PO4.5: 7 residues within 4Å: Chain B: N.70, M.71, D.72, T.267, N.268, S.269, K.310 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:N.70, B:N.70, B:M.71, B:D.72, B:D.72, B:T.267, B:N.268, B:N.268, B:S.269 Salt bridges: B:K.310 PO4.7: 6 residues within 4Å: Chain C: R.52, V.53, V.55, Y.489, Y.493, F.495 11 PLIP interactions: 11 interactions with chain C Hydrogen bonds: C:Y.493 Water bridges: C:K.44, C:K.44, C:R.46, C:R.52, C:Y.489, C:Y.493, C:Y.493, C:L.494, C:R.496 Salt bridges: C:R.52 PO4.8: 7 residues within 4Å: Chain C: N.70, M.71, D.72, T.267, N.268, S.269, K.310 10 PLIP interactions: 10 interactions with chain C Hydrogen bonds: C:N.70, C:N.70, C:M.71, C:D.72, C:T.267, C:T.267, C:T.267, C:N.268, C:S.269 Salt bridges: C:K.310 PO4.10: 6 residues within 4Å: Chain D: R.52, V.53, V.55, Y.489, Y.493, F.495 11 PLIP interactions: 11 interactions with chain D Hydrogen bonds: D:V.53, D:V.53, D:Y.489 Water bridges: D:R.47, D:R.47, D:Y.493, D:Y.493, D:Y.493, D:Y.493, D:Y.493 Salt bridges: D:R.52 PO4.11: 7 residues within 4Å: Chain D: N.70, M.71, D.72, T.267, N.268, S.269, K.310 8 PLIP interactions: 8 interactions with chain D Hydrogen bonds: D:N.70, D:N.70, D:M.71, D:D.72, D:N.268, D:N.268, D:S.269 Salt bridges: D:K.310

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

EDO.3: 8 residues within 4Å: Chain A: T.445, M.448, D.449, Y.452, R.460, S.461, G.462 Chain C: H.564 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:G.462, C:H.564 Water bridges: A:Y.452 EDO.6: 5 residues within 4Å: Chain B: D.270, Y.271, V.306, D.307, L.330 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Y.271 Water bridges: B:K.272 EDO.9: 8 residues within 4Å: Chain A: H.564 Chain C: T.445, M.448, D.449, Y.452, R.460, S.461, G.462 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:D.449, C:G.462, A:H.564 Water bridges: C:Y.452 EDO.12: 5 residues within 4Å: Chain D: D.270, Y.271, V.306, D.307, L.330 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:Y.271 Water bridges: D:K.272

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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