SMTL ID : 5opm.1

Crystal structure of D52N/R238W cN-II mutant bound to dATP and free phosphate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.68 Å

Oligo State

homo-tetramer

Ligands

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

PO4.1: 8 residues within 4Å: Chain A: N.50, M.51, D.52, T.247, N.248, S.249, K.290 Ligands: MG.2 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:N.50, A:M.51, A:D.52, A:D.52, A:D.52, A:N.248, A:S.249 Water bridges: A:N.50, A:K.290, A:K.290, A:K.290 Salt bridges: A:K.290 PO4.9: 8 residues within 4Å: Chain B: N.50, M.51, D.52, T.247, N.248, S.249, K.290 Ligands: MG.10 12 PLIP interactions: 12 interactions with chain B Hydrogen bonds: B:N.50, B:M.51, B:D.52, B:D.52, B:D.52, B:N.248, B:S.249 Water bridges: B:N.50, B:K.290, B:K.290, B:K.290 Salt bridges: B:K.290 PO4.17: 8 residues within 4Å: Chain C: N.50, M.51, D.52, T.247, N.248, S.249, K.290 Ligands: MG.18 12 PLIP interactions: 12 interactions with chain C Hydrogen bonds: C:N.50, C:M.51, C:D.52, C:D.52, C:T.247, C:N.248, C:S.249 Water bridges: C:N.50, C:K.290, C:K.290, C:K.290 Salt bridges: C:K.290 PO4.25: 8 residues within 4Å: Chain D: N.50, M.51, D.52, T.247, N.248, S.249, K.290 Ligands: MG.26 12 PLIP interactions: 12 interactions with chain D Hydrogen bonds: D:N.50, D:M.51, D:D.52, D:D.52, D:T.247, D:N.248, D:S.249 Water bridges: D:N.50, D:K.290, D:K.290, D:K.290 Salt bridges: D:K.290

8 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: N.50, D.52, D.349 Ligands: PO4.1 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.52, A:D.349, H2O.2, H2O.3 MG.3: 5 residues within 4Å: Chain A: K.360, Y.447 Ligands: DTP.4, MG.19, DTP.20 No protein-ligand interaction detected (PLIP) MG.10: 4 residues within 4Å: Chain B: N.50, D.52, D.349 Ligands: PO4.9 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.52, B:D.349, H2O.15, H2O.16 MG.11: 5 residues within 4Å: Chain B: K.360, Y.447 Ligands: DTP.12, MG.27, DTP.28 No protein-ligand interaction detected (PLIP) MG.18: 4 residues within 4Å: Chain C: N.50, D.52, D.349 Ligands: PO4.17 4 PLIP interactions: 2 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.52, C:D.349, H2O.29, H2O.30 MG.19: 5 residues within 4Å: Chain C: K.360, Y.447 Ligands: MG.3, DTP.4, DTP.20 No protein-ligand interaction detected (PLIP) MG.26: 4 residues within 4Å: Chain D: N.50, D.52, D.349 Ligands: PO4.25 4 PLIP interactions: 2 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:D.52, D:D.349, H2O.42, H2O.43 MG.27: 5 residues within 4Å: Chain D: K.360, Y.447 Ligands: MG.11, DTP.12, DTP.28 No protein-ligand interaction detected (PLIP)

4 x DTP: 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE(Non-covalent)

DTP.4: 15 residues within 4Å: Chain A: R.142, D.143, I.150, N.152, F.352, L.356, K.360, Q.443, R.446, Y.447 Chain C: K.360, R.446 Ligands: MG.3, MG.19, DTP.20 16 PLIP interactions: 13 interactions with chain A, 3 interactions with chain C Hydrophobic interactions: A:F.352 Hydrogen bonds: A:R.142, A:N.152, A:N.152, A:Q.443, A:Y.447, A:Y.447 Water bridges: A:I.150 Salt bridges: A:R.142, A:R.142, A:K.360, A:R.446, C:K.360, C:K.360, C:R.446 pi-Stacking: A:F.352 DTP.12: 15 residues within 4Å: Chain B: R.142, D.143, I.150, N.152, F.352, L.356, K.360, Q.443, R.446, Y.447 Chain D: K.360, R.446 Ligands: MG.11, MG.27, DTP.28 16 PLIP interactions: 13 interactions with chain B, 3 interactions with chain D Hydrophobic interactions: B:F.352 Hydrogen bonds: B:R.142, B:N.152, B:N.152, B:Q.443, B:Y.447, B:Y.447 Water bridges: B:I.150 Salt bridges: B:R.142, B:R.142, B:K.360, B:R.446, D:K.360, D:K.360, D:R.446 pi-Stacking: B:F.352 DTP.20: 15 residues within 4Å: Chain A: K.360, R.446 Chain C: R.142, D.143, I.150, N.152, F.352, L.356, K.360, Q.443, R.446, Y.447 Ligands: MG.3, DTP.4, MG.19 15 PLIP interactions: 12 interactions with chain C, 3 interactions with chain A Hydrophobic interactions: C:F.352 Hydrogen bonds: C:R.142, C:N.152, C:N.152, C:Q.443, C:Y.447 Water bridges: C:I.150 Salt bridges: C:R.142, C:R.142, C:K.360, C:R.446, A:K.360, A:K.360, A:R.446 pi-Stacking: C:F.352 DTP.28: 15 residues within 4Å: Chain B: K.360, R.446 Chain D: R.142, D.143, I.150, N.152, F.352, L.356, K.360, Q.443, R.446, Y.447 Ligands: MG.11, DTP.12, MG.27 15 PLIP interactions: 12 interactions with chain D, 3 interactions with chain B Hydrophobic interactions: D:F.352 Hydrogen bonds: D:R.142, D:N.152, D:N.152, D:Q.443, D:Y.447 Water bridges: D:I.150 Salt bridges: D:R.142, D:R.142, D:K.360, D:R.446, B:K.360, B:K.360, B:R.446 pi-Stacking: D:F.352

16 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 7 residues within 4Å: Chain A: V.33, V.35, Y.461, Y.465, L.466, F.467, R.468 Ligand excluded by PLIP GOL.6: 6 residues within 4Å: Chain A: F.155, R.200, V.203, D.204, H.207, Y.208 Ligand excluded by PLIP GOL.7: 5 residues within 4Å: Chain A: L.117, T.417, S.433, G.434, R.436 Ligand excluded by PLIP GOL.8: 8 residues within 4Å: Chain A: D.52, Y.63, F.155, H.207, Y.208, K.213, S.249, Y.253 Ligand excluded by PLIP GOL.13: 7 residues within 4Å: Chain B: V.33, V.35, Y.461, Y.465, L.466, F.467, R.468 Ligand excluded by PLIP GOL.14: 6 residues within 4Å: Chain B: F.155, R.200, V.203, D.204, H.207, Y.208 Ligand excluded by PLIP GOL.15: 5 residues within 4Å: Chain B: L.117, T.417, S.433, G.434, R.436 Ligand excluded by PLIP GOL.16: 8 residues within 4Å: Chain B: D.52, Y.63, F.155, H.207, Y.208, K.213, S.249, Y.253 Ligand excluded by PLIP GOL.21: 7 residues within 4Å: Chain C: V.33, V.35, Y.461, Y.465, L.466, F.467, R.468 Ligand excluded by PLIP GOL.22: 6 residues within 4Å: Chain C: F.155, R.200, V.203, D.204, H.207, Y.208 Ligand excluded by PLIP GOL.23: 5 residues within 4Å: Chain C: L.117, T.417, S.433, G.434, R.436 Ligand excluded by PLIP GOL.24: 8 residues within 4Å: Chain C: D.52, Y.63, F.155, H.207, Y.208, K.213, S.249, Y.253 Ligand excluded by PLIP GOL.29: 7 residues within 4Å: Chain D: V.33, V.35, Y.461, Y.465, L.466, F.467, R.468 Ligand excluded by PLIP GOL.30: 6 residues within 4Å: Chain D: F.155, R.200, V.203, D.204, H.207, Y.208 Ligand excluded by PLIP GOL.31: 5 residues within 4Å: Chain D: L.117, T.417, S.433, G.434, R.436 Ligand excluded by PLIP GOL.32: 8 residues within 4Å: Chain D: D.52, Y.63, F.155, H.207, Y.208, K.213, S.249, Y.253 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hnizda, A. et al., Relapsed acute lymphoblastic leukemia-specific mutations in NT5C2 cluster into hotspots driving intersubunit stimulation. Leukemia (2018)

Release Date

2018-06-13

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