SMTL ID : 6wm7.1 (1 other biounit)

Periplasmic EDTA-binding protein EppA, orthorhombic

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.56 Å

Oligo State

monomer

Ligands

10 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.1: 6 residues within 4Å: Chain A: K.94, M.95, N.96, T.97, D.98, E.558 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:K.94, A:M.95, A:T.97 Water bridges: A:E.558, A:E.558, A:E.558 EDO.2: 8 residues within 4Å: Chain A: L.78, P.79, P.221, A.553, Y.554, N.555, T.556, A.557 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:A.553, A:T.556, A:T.556, A:A.557 EDO.3: 10 residues within 4Å: Chain A: L.105, T.108, Q.111, P.179, F.180, L.181, W.183, A.500, A.501, S.502 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:F.180, A:A.501 EDO.4: 7 residues within 4Å: Chain A: R.56, A.66, L.67, G.68, N.69, N.70, D.447 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.69, A:N.70 Water bridges: A:R.56, A:R.56, A:R.56 EDO.5: 9 residues within 4Å: Chain A: V.87, Y.155, M.188, Q.463, Q.464, V.465, F.466, Q.549, L.550 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:V.465, A:Q.549 Water bridges: A:F.466 EDO.6: 3 residues within 4Å: Chain A: R.408, G.452, N.453 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.408 Water bridges: A:N.453 EDO.7: 4 residues within 4Å: Chain A: K.46, G.47, G.48, D.250 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.48 Water bridges: A:K.46 EDO.8: 9 residues within 4Å: Chain A: F.91, P.302, S.303, A.304, L.357, N.359, Q.529, P.547, N.548 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.359, A:P.547 EDO.9: 9 residues within 4Å: Chain A: F.52, A.53, V.54, T.55, A.71, V.72, T.75, Q.263, Y.276 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:T.55, A:T.55, A:A.71 Water bridges: A:A.53, A:T.55, A:Q.263 EDO.10: 8 residues within 4Å: Chain A: Y.276, Q.278, S.303, N.305, Y.415, L.530, P.531, T.532 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.278, A:N.305

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

SO4.11: 3 residues within 4Å: Chain A: R.56, T.445, D.447 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.447 Water bridges: A:R.56, A:R.56 Salt bridges: A:R.56 SO4.12: 5 residues within 4Å: Chain A: R.143, A.153, S.154, Y.155, Q.473 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:S.154, A:Y.155, A:Q.473 Water bridges: A:R.143, A:R.143, A:R.143, A:G.156 Salt bridges: A:R.143

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lewis, K.M. et al., The Structural Basis of the Binding of Various Aminopolycarboxylates by the Periplasmic EDTA-Binding Protein EppA from Chelativorans sp. BNC1. Int J Mol Sci (2020)

Release Date

2020-11-18

Peptides

Extracellular solute-binding protein, family 5: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Extracellular solute-binding protein, family 5

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