SMTL ID : 4h4b.2 (1 other biounit)

Human cytosolic 5'-nucleotidase II in complex with Anthraquinone-2,6- disulfonic acid

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.90 Å

Oligo State

homo-dimer

Ligands

2 x 11H: 9,10-dioxo-9,10-dihydroanthracene-2,6-disulfonic acid(Non-covalent)

11H.1: 8 residues within 4Å: Chain A: R.163, I.171, N.173, K.311, P.312, H.371, F.373, Q.472 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:F.373 Hydrogen bonds: A:N.173, A:Q.472 Salt bridges: A:R.163 pi-Stacking: A:F.373, A:F.373 11H.9: 8 residues within 4Å: Chain B: R.163, I.171, N.173, K.311, P.312, H.371, F.373, Q.472 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:F.373 Hydrogen bonds: B:N.173, B:Q.472 Salt bridges: B:R.163 pi-Stacking: B:F.373, B:F.373

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 9 residues within 4Å: Chain A: Q.299, F.302, D.303, L.304, I.305, Q.341, H.342, G.343, I.344 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:I.305, A:G.343 GOL.10: 9 residues within 4Å: Chain B: Q.299, F.302, D.303, L.304, I.305, Q.341, H.342, G.343, I.344 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:I.305, B:H.342, B:G.343

2 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 6 residues within 4Å: Chain A: D.71, D.73, T.75, D.370, D.375 Ligands: SO4.5 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.71, A:D.73, A:D.370, H2O.1, H2O.2 MG.11: 6 residues within 4Å: Chain B: D.71, D.73, T.75, D.370, D.375 Ligands: SO4.13 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.71, B:D.73, B:D.370, H2O.3, H2O.5

10 x SO4: SULFATE ION(Non-functional Binders)

SO4.4: 8 residues within 4Å: Chain A: R.163, L.377, L.468, Q.472, R.475, Y.476 Chain B: K.381, R.475 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:Q.472, A:R.475, A:Y.476 Salt bridges: A:R.163, B:K.381, B:R.475 SO4.5: 3 residues within 4Å: Chain A: N.269, H.371 Ligands: MG.3 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.269 Water bridges: A:K.311, A:K.311 Salt bridges: A:H.371 SO4.6: 2 residues within 4Å: Chain A: R.95, W.226 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.95 SO4.7: 4 residues within 4Å: Chain A: G.149, P.150, R.153, K.159 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.149 Salt bridges: A:R.153, A:K.159 SO4.8: 5 residues within 4Å: Chain A: N.136, L.137, K.159, R.465 Chain B: K.363 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Water bridges: A:R.465 Salt bridges: A:R.465, B:K.363 SO4.12: 8 residues within 4Å: Chain A: K.381, R.475 Chain B: R.163, L.377, L.468, Q.472, R.475, Y.476 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:Q.472, B:R.475 Salt bridges: B:R.163, A:K.381, A:R.475 SO4.13: 3 residues within 4Å: Chain B: N.269, H.371 Ligands: MG.11 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.269 Water bridges: B:K.311, B:K.311 Salt bridges: B:H.371 SO4.14: 2 residues within 4Å: Chain B: R.95, W.226 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:R.95 SO4.15: 4 residues within 4Å: Chain B: G.149, P.150, R.153, K.159 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:G.149 Salt bridges: B:R.153, B:K.159 SO4.16: 5 residues within 4Å: Chain A: K.363 Chain B: N.136, L.137, K.159, R.465 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Water bridges: B:R.465 Salt bridges: B:R.465, A:K.363

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Jordheim, L.P. et al., Identification and characterization of inhibitors of cytoplasmic 5'-nucleotidase cN-II issued from virtual screening. Biochem Pharmacol (2013)

Release Date

2012-12-26

Peptides

Cytosolic purine 5'-nucleotidase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Cytosolic purine 5'-nucleotidase

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