SMTL ID : 5opk.1

Crystal structure of D52N/R367Q cN-II mutant bound to dATP and free phosphate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.74 Å

Oligo State

homo-tetramer

Ligands

36 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 7 residues within 4Å: Chain A: D.250, Y.251, V.286, D.287, G.308, K.309, L.310 Ligand excluded by PLIP GOL.2: 8 residues within 4Å: Chain A: H.476, E.477 Chain C: E.376, W.380, Y.424, S.429, F.431, R.432 Ligand excluded by PLIP GOL.3: 8 residues within 4Å: Chain A: F.281, D.282, L.283, I.284, Q.320, H.321, G.322, I.323 Ligand excluded by PLIP GOL.4: 6 residues within 4Å: Chain A: R.26, R.32, V.33, V.35, Y.461, Y.465 Ligand excluded by PLIP GOL.5: 6 residues within 4Å: Chain A: T.95, E.372, E.376, Y.424, G.428, L.430 Ligand excluded by PLIP GOL.6: 8 residues within 4Å: Chain A: T.54, L.55, V.57, V.225, D.227, S.454, F.455, I.456 Ligand excluded by PLIP GOL.7: 6 residues within 4Å: Chain A: Y.149, I.150, N.152, H.350, F.352 Ligands: DTP.13 Ligand excluded by PLIP GOL.8: 5 residues within 4Å: Chain A: F.155, H.207, Y.208, N.248 Ligands: PO4.10 Ligand excluded by PLIP GOL.9: 5 residues within 4Å: Chain A: D.255, T.259, P.276, W.277, Q.278 Ligand excluded by PLIP GOL.14: 7 residues within 4Å: Chain B: D.250, Y.251, V.286, D.287, G.308, K.309, L.310 Ligand excluded by PLIP GOL.15: 8 residues within 4Å: Chain B: H.476, E.477 Chain D: E.376, W.380, Y.424, S.429, F.431, R.432 Ligand excluded by PLIP GOL.16: 8 residues within 4Å: Chain B: F.281, D.282, L.283, I.284, Q.320, H.321, G.322, I.323 Ligand excluded by PLIP GOL.17: 6 residues within 4Å: Chain B: R.26, R.32, V.33, V.35, Y.461, Y.465 Ligand excluded by PLIP GOL.18: 6 residues within 4Å: Chain B: T.95, E.372, E.376, Y.424, G.428, L.430 Ligand excluded by PLIP GOL.19: 8 residues within 4Å: Chain B: T.54, L.55, V.57, V.225, D.227, S.454, F.455, I.456 Ligand excluded by PLIP GOL.20: 6 residues within 4Å: Chain B: Y.149, I.150, N.152, H.350, F.352 Ligands: DTP.26 Ligand excluded by PLIP GOL.21: 5 residues within 4Å: Chain B: F.155, H.207, Y.208, N.248 Ligands: PO4.23 Ligand excluded by PLIP GOL.22: 5 residues within 4Å: Chain B: D.255, T.259, P.276, W.277, Q.278 Ligand excluded by PLIP GOL.27: 7 residues within 4Å: Chain C: D.250, Y.251, V.286, D.287, G.308, K.309, L.310 Ligand excluded by PLIP GOL.28: 8 residues within 4Å: Chain A: E.376, W.380, Y.424, S.429, F.431, R.432 Chain C: H.476, E.477 Ligand excluded by PLIP GOL.29: 8 residues within 4Å: Chain C: F.281, D.282, L.283, I.284, Q.320, H.321, G.322, I.323 Ligand excluded by PLIP GOL.30: 6 residues within 4Å: Chain C: R.26, R.32, V.33, V.35, Y.461, Y.465 Ligand excluded by PLIP GOL.31: 6 residues within 4Å: Chain C: T.95, E.372, E.376, Y.424, G.428, L.430 Ligand excluded by PLIP GOL.32: 8 residues within 4Å: Chain C: T.54, L.55, V.57, V.225, D.227, S.454, F.455, I.456 Ligand excluded by PLIP GOL.33: 6 residues within 4Å: Chain C: Y.149, I.150, N.152, H.350, F.352 Ligands: DTP.39 Ligand excluded by PLIP GOL.34: 5 residues within 4Å: Chain C: F.155, H.207, Y.208, N.248 Ligands: PO4.36 Ligand excluded by PLIP GOL.35: 5 residues within 4Å: Chain C: D.255, T.259, P.276, W.277, Q.278 Ligand excluded by PLIP GOL.40: 7 residues within 4Å: Chain D: D.250, Y.251, V.286, D.287, G.308, K.309, L.310 Ligand excluded by PLIP GOL.41: 8 residues within 4Å: Chain B: E.376, W.380, Y.424, S.429, F.431, R.432 Chain D: H.476, E.477 Ligand excluded by PLIP GOL.42: 8 residues within 4Å: Chain D: F.281, D.282, L.283, I.284, Q.320, H.321, G.322, I.323 Ligand excluded by PLIP GOL.43: 6 residues within 4Å: Chain D: R.26, R.32, V.33, V.35, Y.461, Y.465 Ligand excluded by PLIP GOL.44: 6 residues within 4Å: Chain D: T.95, E.372, E.376, Y.424, G.428, L.430 Ligand excluded by PLIP GOL.45: 8 residues within 4Å: Chain D: T.54, L.55, V.57, V.225, D.227, S.454, F.455, I.456 Ligand excluded by PLIP GOL.46: 6 residues within 4Å: Chain D: Y.149, I.150, N.152, H.350, F.352 Ligands: DTP.52 Ligand excluded by PLIP GOL.47: 5 residues within 4Å: Chain D: F.155, H.207, Y.208, N.248 Ligands: PO4.49 Ligand excluded by PLIP GOL.48: 5 residues within 4Å: Chain D: D.255, T.259, P.276, W.277, Q.278 Ligand excluded by PLIP

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

PO4.10: 9 residues within 4Å: Chain A: N.50, M.51, D.52, T.247, N.248, S.249, K.290 Ligands: GOL.8, MG.11 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 PO4.23: 9 residues within 4Å: Chain B: N.50, M.51, D.52, T.247, N.248, S.249, K.290 Ligands: GOL.21, MG.24 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 PO4.36: 9 residues within 4Å: Chain C: N.50, M.51, D.52, T.247, N.248, S.249, K.290 Ligands: GOL.34, MG.37 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 PO4.49: 9 residues within 4Å: Chain D: N.50, M.51, D.52, T.247, N.248, S.249, K.290 Ligands: GOL.47, MG.50 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.11: 4 residues within 4Å: Chain A: N.50, D.52, D.349 Ligands: PO4.10 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.52, A:D.349, H2O.2, H2O.2 MG.12: 5 residues within 4Å: Chain A: R.446, Y.447 Ligands: DTP.13, MG.38, DTP.39 No protein-ligand interaction detected (PLIP) MG.24: 4 residues within 4Å: Chain B: N.50, D.52, D.349 Ligands: PO4.23 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.52, B:D.349, H2O.13, H2O.13 MG.25: 5 residues within 4Å: Chain B: R.446, Y.447 Ligands: DTP.26, MG.51, DTP.52 No protein-ligand interaction detected (PLIP) MG.37: 4 residues within 4Å: Chain C: N.50, D.52, D.349 Ligands: PO4.36 4 PLIP interactions: 2 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.52, C:D.349, H2O.25, H2O.25 MG.38: 5 residues within 4Å: Chain C: R.446, Y.447 Ligands: MG.12, DTP.13, DTP.39 No protein-ligand interaction detected (PLIP) MG.50: 4 residues within 4Å: Chain D: N.50, D.52, D.349 Ligands: PO4.49 4 PLIP interactions: 2 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:D.52, D:D.349, H2O.36, H2O.36 MG.51: 5 residues within 4Å: Chain D: R.446, Y.447 Ligands: MG.25, DTP.26, DTP.52 No protein-ligand interaction detected (PLIP)

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

DTP.13: 16 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: GOL.7, MG.12, MG.38, DTP.39 19 PLIP interactions: 13 interactions with chain A, 6 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:R.142, C:R.446, C:R.446, C:Y.447 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.26: 16 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: GOL.20, MG.25, MG.51, DTP.52 18 PLIP interactions: 5 interactions with chain D, 13 interactions with chain B Water bridges: D:R.446, D:Y.447, B:R.142 Salt bridges: D:K.360, D:K.360, D:R.446, B:R.142, B:R.142, B:K.360, B:R.446 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 pi-Stacking: B:F.352 DTP.39: 16 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.12, DTP.13, GOL.33, MG.38 19 PLIP interactions: 14 interactions with chain C, 5 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:R.142, C:R.142, C:Y.447, A:R.446, A:R.446 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.52: 16 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.25, DTP.26, GOL.46, MG.51 19 PLIP interactions: 14 interactions with chain D, 5 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:R.142, D:R.142, D:Y.447, B:R.446, B:R.446 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

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