SMTL ID : 4ohf.3 (2 other biounits)

Crystal structure of cytosolic nucleotidase II (LPG0095) in complex with GMP from Legionella pneumophila, NORTHEAST STRUCTURAL GENOMICS CONSORTIUM TARGET LGR1

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.53 Å

Oligo State

homo-dimer

Ligands

1 x 5GP: GUANOSINE-5'-MONOPHOSPHATE(Non-covalent)

5GP.1: 9 residues within 4Å: Chain A: R.86, Y.87, D.308, Y.421, R.425 Chain B: R.86, Y.87, Y.418, Y.421 10 PLIP interactions: 3 interactions with chain B, 7 interactions with chain A Hydrogen bonds: B:R.86, A:R.86, A:R.86, A:R.86, A:Y.421, A:R.425 Water bridges: B:Y.421 pi-Stacking: B:Y.421, A:Y.421 pi-Cation interactions: A:Y.421

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

PO4.2: 8 residues within 4Å: Chain A: D.23, M.24, D.25, T.209, N.210, S.211, K.247 Ligands: MG.4 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:D.23, A:M.24, A:D.25, A:T.209, A:T.209, A:N.210, A:S.211 Salt bridges: A:K.247 PO4.3: 8 residues within 4Å: Chain A: R.10, K.313, W.318, R.319, T.320, F.426, A.427, C.428 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.320, A:T.320 Salt bridges: A:R.10, A:K.313, A:R.319 PO4.5: 9 residues within 4Å: Chain B: D.23, M.24, D.25, L.208, T.209, N.210, S.211, K.247 Ligands: MG.7 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:D.23, B:M.24, B:D.25, B:D.25, B:D.25, B:T.209, B:N.210, B:S.211 Salt bridges: B:K.247 PO4.6: 8 residues within 4Å: Chain A: Y.113 Chain B: R.10, K.313, R.319, T.320, F.426, A.427, C.428 9 PLIP interactions: 7 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:T.320, B:T.320, B:T.320, B:C.428, A:Y.113, A:Y.113 Salt bridges: B:R.10, B:K.313, B:R.319

2 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 4 residues within 4Å: Chain A: D.23, D.25, D.303 Ligands: PO4.2 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.23, A:D.23, A:D.25, A:D.303, H2O.2 MG.7: 4 residues within 4Å: Chain B: D.23, D.25, D.303 Ligands: PO4.5 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.23, B:D.23, B:D.25, B:D.303, H2O.4

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Srinivasan, B. et al., Allosteric regulation and substrate activation in cytosolic nucleotidase II from Legionella pneumophila. Febs J. (2014)

Release Date

2014-02-26

Peptides

Cytosolic IMP-GMP specific 5'-nucleotidase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

Cytosolic IMP-GMP specific 5'-nucleotidase

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