SMTL ID : 2j2c.1

Crystal structure of Human Cytosolic 5'-Nucleotidase II (NT5C2, cN-II)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-dimer

Ligands

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 7 residues within 4Å: Chain A: P.115, T.116, E.393, E.397, Y.453, G.457, L.459 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:Y.453 Water bridges: A:S.112, A:S.112, A:P.115, A:T.116, A:R.117, A:E.393 GOL.9: 7 residues within 4Å: Chain B: P.115, T.116, E.393, E.397, Y.453, G.457, L.459 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:E.397, B:Y.453 Water bridges: B:S.112, B:S.112, B:P.115, B:R.117, B:E.393

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

SO4.2: 3 residues within 4Å: Chain A: R.163, Q.472, Y.476 11 PLIP interactions: 9 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:Q.472, A:Y.476, A:Y.476 Water bridges: A:A.133, A:R.163, A:R.163, A:R.163, A:R.475, B:K.381 Salt bridges: A:R.163, B:K.381 SO4.3: 3 residues within 4Å: Chain A: N.269, H.371 Ligands: MG.8 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:N.269 Water bridges: A:D.71, A:D.71, A:D.71, A:D.73, A:K.311, A:D.375 Salt bridges: A:H.371 SO4.4: 5 residues within 4Å: Chain A: K.44, R.47, R.48, Y.494, R.497 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Y.494, A:R.497 Salt bridges: A:K.44, A:R.47, A:R.48 SO4.5: 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 SO4.6: 4 residues within 4Å: Chain A: G.149, P.150, R.153, K.159 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.153, A:K.159 SO4.7: 2 residues within 4Å: Chain A: R.95, W.226 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.95, A:K.230 SO4.10: 3 residues within 4Å: Chain B: R.163, Q.472, Y.476 10 PLIP interactions: 8 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:Q.472, B:Y.476 Water bridges: B:A.133, B:R.163, B:R.163, B:R.163, B:R.475, A:K.381 Salt bridges: B:R.163, A:K.381 SO4.11: 3 residues within 4Å: Chain B: N.269, H.371 Ligands: MG.16 13 PLIP interactions: 13 interactions with chain B Hydrogen bonds: B:N.269 Water bridges: B:D.71, B:D.71, B:D.71, B:T.174, B:T.268, B:S.270, B:K.311, B:H.371, B:H.371, B:H.371, B:D.375 Salt bridges: B:H.371 SO4.12: 5 residues within 4Å: Chain B: K.44, R.47, R.48, Y.494, R.497 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.497 Salt bridges: B:K.44, B:R.47, B:R.48 SO4.13: 4 residues within 4Å: Chain A: K.363 Chain B: N.136, K.159, R.465 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Salt bridges: A:K.363, B:R.465 SO4.14: 4 residues within 4Å: Chain B: G.149, P.150, R.153, K.159 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:R.153, B:K.159 SO4.15: 2 residues within 4Å: Chain B: R.95, W.226 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:R.95, B:K.230

2 x MG: MAGNESIUM ION(Non-covalent)

MG.8: 4 residues within 4Å: Chain A: D.71, D.73, D.370 Ligands: SO4.3 6 PLIP interactions: 3 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.71, A:D.73, A:D.370, H2O.15, H2O.15, H2O.18 MG.16: 4 residues within 4Å: Chain B: D.71, D.73, D.370 Ligands: SO4.11 6 PLIP interactions: 3 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.71, B:D.73, B:D.370, H2O.32, H2O.32, H2O.35

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

2006-09-19

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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