SMTL ID : 2jc9.1

Crystal structure of Human Cytosolic 5'-Nucleotidase II in complex with adenosine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

homo-dimer

Ligands

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 8 residues within 4Å: Chain A: F.302, D.303, I.305, L.340, Q.341, H.342, G.343, I.344 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:H.342, A:G.343, A:I.344 Water bridges: A:I.305, A:G.343 GOL.2: 4 residues within 4Å: Chain A: D.26, K.80, S.81, E.83 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.81 Water bridges: A:K.80, A:K.80 GOL.11: 8 residues within 4Å: Chain B: F.302, D.303, I.305, L.340, Q.341, H.342, G.343, I.344 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:H.342, B:G.343, B:I.344 Water bridges: B:I.305, B:G.343 GOL.12: 4 residues within 4Å: Chain B: D.26, K.80, S.81, E.83 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:S.81 Water bridges: B:D.26, B:D.26, B:K.80, B:K.80

2 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 3 residues within 4Å: Chain A: D.71, D.73, D.370 6 PLIP interactions: 3 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.71, A:D.73, A:D.370, H2O.16, H2O.19, H2O.19 MG.13: 3 residues within 4Å: Chain B: D.71, D.73, D.370 6 PLIP interactions: 3 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.71, B:D.73, B:D.370, H2O.35, H2O.38, H2O.38

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

SO4.4: 4 residues within 4Å: Chain A: R.163, Q.472, Y.476 Ligands: ADN.9 11 PLIP interactions: 7 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:Q.472, A:Y.476, A:Y.476 Water bridges: A:K.381, A:K.381, B:K.381, B:K.381, B:K.381, B:K.381 Salt bridges: A:R.163, A:K.381 SO4.5: 2 residues within 4Å: Chain A: N.269, H.371 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:N.269 Water bridges: A:D.71, A:D.71, A:D.73, A:S.270, A:K.311, A:D.370, A:D.375 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: 4 residues within 4Å: Chain A: N.136, K.159, R.465 Chain B: K.363 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Salt bridges: A:R.465, B:K.363 SO4.14: 4 residues within 4Å: Chain B: R.163, Q.472, Y.476 Ligands: ADN.19 12 PLIP interactions: 5 interactions with chain A, 7 interactions with chain B Water bridges: A:K.381, A:K.381, A:K.381, A:K.381, A:K.381, B:K.381, B:R.475, B:R.475 Hydrogen bonds: B:Q.472, B:Y.476 Salt bridges: B:R.163, B:K.381 SO4.15: 2 residues within 4Å: Chain B: N.269, H.371 14 PLIP interactions: 14 interactions with chain B Hydrogen bonds: B:N.269 Water bridges: B:D.71, B:D.71, B:D.73, B:T.174, B:T.268, B:S.270, B:K.311, B:D.370, B:H.371, B:H.371, B:H.371, B:D.375 Salt bridges: B:H.371 SO4.16: 2 residues within 4Å: Chain B: R.95, W.226 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:R.95 SO4.17: 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 SO4.18: 4 residues within 4Å: Chain A: K.363 Chain B: N.136, K.159, R.465 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Salt bridges: B:R.465, A:K.363

4 x ADN: ADENOSINE(Non-covalent)

ADN.9: 8 residues within 4Å: Chain A: R.163, D.164, T.166, I.171, N.173, F.373, Q.472 Ligands: SO4.4 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:R.163, A:N.173, A:N.173, A:Q.472 Water bridges: A:T.166, A:I.171, A:K.378, A:K.378 pi-Stacking: A:F.373 ADN.10: 7 residues within 4Å: Chain A: F.146, I.147, R.148, K.443, H.447, M.451, M.455 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:I.147, A:R.148, A:R.148, A:M.455 Water bridges: A:I.147, A:D.450 pi-Stacking: A:F.146, A:H.447 ADN.19: 8 residues within 4Å: Chain B: R.163, D.164, T.166, I.171, N.173, F.373, Q.472 Ligands: SO4.14 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:R.163, B:N.173, B:N.173, B:Q.472 Water bridges: B:T.166, B:I.171, B:K.378, B:K.378 pi-Stacking: B:F.373 ADN.20: 7 residues within 4Å: Chain B: F.146, I.147, R.148, K.443, H.447, M.451, M.455 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:I.147, B:R.148, B:R.148, B:M.455 Water bridges: B:I.147 pi-Stacking: B:F.146, B:H.447

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wallden, K. et al., Crystal Structure of Human Cytosolic 5'-Nucleotidase II: Insights Into Allosteric Regulation and Substrate Recognition. J.Biol.Chem. (2007)

Release Date

2007-01-02

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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