SMTL ID : 5u7h.1 (1 other biounit)

Ni-bound dihydroneopterin triphosphate pyrophosphohydrolase from E. coli

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

monomer

Ligands

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

SO4.1: 4 residues within 4Å: Chain A: F.81, E.82, R.97, W.136 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.82 Water bridges: A:R.97, A:R.97 Salt bridges: A:R.97 SO4.2: 12 residues within 4Å: Chain A: K.7, T.40, G.41, S.42, E.56, E.60, E.117 Ligands: SO4.3, NI.4, NI.5, NI.6, NI.7 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:S.42 Water bridges: A:R.29, A:R.29, A:R.29, A:S.42, A:S.42, A:E.44, A:R.55, A:R.90 Salt bridges: A:K.7 SO4.3: 5 residues within 4Å: Chain A: K.7, R.29, D.31, R.90 Ligands: SO4.2 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.29 Water bridges: A:R.29, A:R.90 Salt bridges: A:K.7, A:R.90

5 x NI: NICKEL (II) ION(Non-covalent)

NI.4: 8 residues within 4Å: Chain A: T.40, E.56, E.60, E.117 Ligands: SO4.2, NI.5, NI.6, NI.7 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.56, A:E.60, A:E.117, H2O.2, H2O.3 NI.5: 7 residues within 4Å: Chain A: T.40, G.41, E.56, E.60, E.117 Ligands: SO4.2, NI.4 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:T.40, A:E.60, A:E.117, H2O.2, H2O.2 NI.6: 5 residues within 4Å: Chain A: R.55, E.56 Ligands: SO4.2, NI.4, NI.7 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:E.56, H2O.2, H2O.3, H2O.3, H2O.4 NI.7: 4 residues within 4Å: Chain A: E.117 Ligands: SO4.2, NI.4, NI.6 No protein-ligand interaction detected (PLIP) NI.8: 1 residues within 4Å: Chain A: H.109 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:H.109

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hill, S.E. et al., Metal ion coordination in the E. coli Nudix hydrolase dihydroneopterin triphosphate pyrophosphatase: New clues into catalytic mechanism. PLoS ONE (2017)

Release Date

2017-06-21

Peptides

Dihydroneopterin triphosphate diphosphatase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Dihydroneopterin triphosphate diphosphatase

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