SMTL ID : 6dd3.1

Crystal structure of the double mutant (D52N/D407A) of NT5C2-537X in the active state

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.98 Å

Oligo State

homo-tetramer

Ligands

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

PO4.1: 7 residues within 4Å: Chain A: N.52, M.53, D.54, T.249, N.250, S.251, K.292 Ligand excluded by PLIP PO4.2: 5 residues within 4Å: Chain A: R.144, L.358, Q.453, R.456, Y.457 Ligand excluded by PLIP PO4.3: 4 residues within 4Å: Chain A: G.130, P.131, R.134, K.140 Ligand excluded by PLIP PO4.4: 4 residues within 4Å: Chain A: N.117, K.140, R.446 Chain C: K.344 Ligand excluded by PLIP PO4.7: 7 residues within 4Å: Chain B: N.52, M.53, D.54, T.249, N.250, S.251, K.292 Ligand excluded by PLIP PO4.8: 5 residues within 4Å: Chain B: R.144, L.358, Q.453, R.456, Y.457 Ligand excluded by PLIP PO4.9: 4 residues within 4Å: Chain B: G.130, P.131, R.134, K.140 Ligand excluded by PLIP PO4.10: 4 residues within 4Å: Chain B: N.117, K.140, R.446 Chain D: K.344 Ligand excluded by PLIP PO4.13: 7 residues within 4Å: Chain C: N.52, M.53, D.54, T.249, N.250, S.251, K.292 Ligand excluded by PLIP PO4.14: 5 residues within 4Å: Chain C: R.144, L.358, Q.453, R.456, Y.457 Ligand excluded by PLIP PO4.15: 4 residues within 4Å: Chain C: G.130, P.131, R.134, K.140 Ligand excluded by PLIP PO4.16: 4 residues within 4Å: Chain A: K.344 Chain C: N.117, K.140, R.446 Ligand excluded by PLIP PO4.19: 7 residues within 4Å: Chain D: N.52, M.53, D.54, T.249, N.250, S.251, K.292 Ligand excluded by PLIP PO4.20: 5 residues within 4Å: Chain D: R.144, L.358, Q.453, R.456, Y.457 Ligand excluded by PLIP PO4.21: 4 residues within 4Å: Chain D: G.130, P.131, R.134, K.140 Ligand excluded by PLIP PO4.22: 4 residues within 4Å: Chain B: K.344 Chain D: N.117, K.140, R.446 Ligand excluded by PLIP

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 6 residues within 4Å: Chain A: D.252, Y.253, V.288, D.289, G.310, L.312 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.253 Water bridges: A:S.251, A:K.254, A:D.289 GOL.6: 8 residues within 4Å: Chain A: F.283, D.284, I.286, L.321, Q.322, H.323, G.324, I.325 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:F.283, A:Q.322, A:G.324 Water bridges: A:I.286 GOL.11: 6 residues within 4Å: Chain B: D.252, Y.253, V.288, D.289, G.310, L.312 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Y.253 Water bridges: B:S.251, B:K.254, B:D.289 GOL.12: 8 residues within 4Å: Chain B: F.283, D.284, I.286, L.321, Q.322, H.323, G.324, I.325 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:F.283, B:Q.322, B:G.324 Water bridges: B:I.286 GOL.17: 6 residues within 4Å: Chain C: D.252, Y.253, V.288, D.289, G.310, L.312 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:Y.253 Water bridges: C:S.251, C:K.254, C:D.289 GOL.18: 8 residues within 4Å: Chain C: F.283, D.284, I.286, L.321, Q.322, H.323, G.324, I.325 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:F.283, C:Q.322, C:G.324 Water bridges: C:I.286, C:H.323 GOL.23: 6 residues within 4Å: Chain D: D.252, Y.253, V.288, D.289, G.310, L.312 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:Y.253 Water bridges: D:S.251, D:K.254, D:D.289 GOL.24: 8 residues within 4Å: Chain D: F.283, D.284, I.286, L.321, Q.322, H.323, G.324, I.325 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:F.283, D:Q.322, D:G.324 Water bridges: D:I.286, D:H.323

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