SMTL ID : 6zxu.1 (2 other biounits)

Catabolic reductive dehalogenase NpRdhA, N-terminally tagged.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.73 Å

Oligo State

monomer

Ligands

2 x SF4: IRON/SULFUR CLUSTER(Non-covalent)

SF4.1: 12 residues within 4Å: Chain A: S.499, R.500, I.501, L.506, F.538, C.539, C.542, K.544, C.545, C.595, P.596, W.597 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.539, A:C.542, A:C.545, A:C.595 SF4.2: 11 residues within 4Å: Chain A: C.549, P.550, C.551, I.554, C.575, Y.578, R.579, C.588, R.590, C.591 Ligands: B12.3 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.549, A:C.575, A:C.588, A:C.591

1 x B12: COBALAMIN(Non-covalent)

B12.3: 40 residues within 4Å: Chain A: V.303, D.316, F.317, F.318, W.403, Y.406, Q.430, S.449, Y.453, S.482, V.484, I.485, H.486, N.487, P.488, I.490, L.491, V.498, I.501, G.502, D.503, T.504, L.505, S.514, K.515, S.516, F.562, Y.565, I.567, K.569, A.570, V.572, C.575, T.576, R.579, C.588, G.589, M.592 Ligands: SF4.2, CL.5 44 PLIP interactions: 44 interactions with chain A, Hydrophobic interactions: A:V.303, A:F.317, A:F.318, A:F.318, A:F.318, A:W.403, A:I.485, A:H.486, A:N.487, A:P.488, A:L.491, A:V.498, A:Y.565, A:I.567, A:V.572 Hydrogen bonds: A:F.317, A:Y.406, A:Q.430, A:S.449, A:S.482, A:V.484, A:H.486, A:H.486, A:I.501, A:D.503, A:D.503, A:T.504, A:L.505, A:L.505, A:K.515, A:S.516, A:S.516, A:K.569, A:R.579, A:C.588 Water bridges: A:Y.453, A:S.514, A:Y.565, A:Y.565, A:C.588, A:Y.680, A:Q.685 Salt bridges: A:K.569 pi-Stacking: A:Y.565

1 x NA: SODIUM ION(Non-functional Binders)

NA.4: 3 residues within 4Å: Chain A: C.595, P.596, N.598 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.593

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.5: 5 residues within 4Å: Chain A: F.318, Y.453, K.515, R.579 Ligands: B12.3 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Halliwell, T. et al., Catabolic Reductive Dehalogenase Substrate Complex Structures Underpin Rational Repurposing of Substrate Scope. Microorganisms (2020)

Release Date

2020-09-16

Peptides

Oxidoreductase, NAD-binding/iron-sulfur cluster-binding protein: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Oxidoreductase, NAD-binding/iron-sulfur cluster-binding protein

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