SMTL ID : 4ohf.1 (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 Compare

Method

X-RAY DIFFRACTION 2.53 Å

Oligo State

homo-tetramer

Ligands

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

5GP.1: 8 residues within 4Å: Chain A: R.86, Y.87, D.308, Y.421, R.425 Chain B: R.86, Y.87, Y.421 9 PLIP interactions: 7 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:R.86, A:R.86, A:R.86, A:Y.87, A:R.425, B:R.86 pi-Stacking: A:Y.421, B:Y.421 pi-Cation interactions: A:Y.421 5GP.7: 8 residues within 4Å: Chain C: R.86, Y.87, D.308, Y.421, R.425 Chain D: R.86, Y.87, Y.421 10 PLIP interactions: 3 interactions with chain D, 7 interactions with chain C Hydrogen bonds: D:R.86, D:Y.421, C:R.86, C:R.86, C:R.86, C:Y.421, C:R.425 pi-Stacking: D:Y.421, C:Y.421 pi-Cation interactions: C:Y.421

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

PO4.2: 8 residues within 4Å: Chain A: D.23, M.24, D.25, L.208, T.209, N.210, S.211, K.247 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:M.24, A:D.25, A:D.25, A:D.25, A:D.25, A:N.210 Salt bridges: A:K.247 PO4.3: 7 residues within 4Å: Chain A: R.10, K.313, W.318, R.319, T.320, F.426, C.428 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:T.320, A:T.320, A:T.320 Salt bridges: A:R.10, A:K.313, A:R.319 PO4.4: 8 residues within 4Å: Chain B: D.23, M.24, D.25, T.209, N.210, S.211, K.247 Ligands: MG.6 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:M.24, B:D.25, B:D.25, B:D.25, B:T.209, B:N.210, B:S.211 Water bridges: B:H.26, B:H.26 Salt bridges: B:K.247 PO4.5: 7 residues within 4Å: Chain A: Y.113 Chain B: R.10, K.313, R.319, T.320, F.426, C.428 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:T.320, B:T.320, B:T.320 Salt bridges: B:R.10, B:K.313, B:R.319 PO4.8: 8 residues within 4Å: Chain C: D.23, M.24, D.25, L.208, T.209, N.210, S.211, K.247 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:M.24, C:D.25, C:D.25, C:D.25, C:T.209, C:N.210 Salt bridges: C:K.247 PO4.9: 7 residues within 4Å: Chain C: R.10, K.313, W.318, R.319, T.320, F.426, C.428 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:T.320, C:T.320 Salt bridges: C:R.10, C:K.313, C:R.319 PO4.10: 8 residues within 4Å: Chain D: D.23, M.24, D.25, T.209, N.210, S.211, K.247 Ligands: MG.12 8 PLIP interactions: 8 interactions with chain D Hydrogen bonds: D:M.24, D:D.25, D:D.25, D:D.25, D:D.25, D:N.210, D:S.211 Salt bridges: D:K.247 PO4.11: 7 residues within 4Å: Chain C: Y.113 Chain D: R.10, K.313, R.319, T.320, F.426, C.428 6 PLIP interactions: 5 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:T.320, D:T.320, C:Y.113 Salt bridges: D:R.10, D:K.313, D:R.319

2 x MG: MAGNESIUM ION(Non-covalent)

MG.6: 4 residues within 4Å: Chain B: D.23, D.25, D.303 Ligands: PO4.4 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.5 MG.12: 4 residues within 4Å: Chain D: D.23, D.25, D.303 Ligands: PO4.10 5 PLIP interactions: 4 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.23, D:D.23, D:D.25, D:D.303, H2O.10

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: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Cytosolic IMP-GMP specific 5'-nucleotidase

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