SMTL ID : 4tnn.1

Crystal structure of Escherichia coli protein YodA in complex with Ni - artifact of purification.

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

monomer

Ligands

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

SO4.1: 3 residues within 4Å: Chain A: G.7, K.8, R.149 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.8 Water bridges: A:K.150 Salt bridges: A:K.8, A:R.149 SO4.2: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) SO4.3: 3 residues within 4Å: Chain A: Q.56, T.66, F.67 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.56, A:F.67 Water bridges: A:T.66, A:A.68 SO4.4: 2 residues within 4Å: Chain A: S.165, N.168 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.165, A:N.168 Water bridges: A:S.162 SO4.5: 2 residues within 4Å: Chain A: T.11, E.12 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.12 SO4.6: 2 residues within 4Å: Chain A: T.31, S.33 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.31, A:S.33 Water bridges: A:S.33, A:S.33

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

NI.7: 3 residues within 4Å: Chain A: H.144, H.153, H.193 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.144, A:H.153, A:H.193

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Niedzialkowska, E. et al., Protein purification and crystallization artifacts: The tale usually not told. Protein Sci. (2016)

Release Date

2014-06-25

Peptides

Metal-binding lipocalin: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Metal-binding lipocalin

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