SMTL ID : 6zxx.3 (2 other biounits)

Catabolic reductive dehalogenase NpRdhA, N-terminally tagged.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.99 Å

Oligo State

monomer

Ligands

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

SF4.1: 10 residues within 4Å: Chain A: R.500, I.501, L.506, F.538, C.539, C.542, 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: 10 residues within 4Å: Chain A: C.549, P.550, C.551, 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: 41 residues within 4Å: Chain A: V.303, G.315, D.316, F.317, F.318, 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, K.569, A.570, V.572, C.575, T.576, R.579, C.588, G.589, M.592 Ligands: SF4.2, QSH.5, QSB.6, BR.7 35 PLIP interactions: 35 interactions with chain A, Hydrophobic interactions: A:V.303, A:F.317, A:F.318, A:F.318, A:F.318, A:I.485, A:H.486, A:N.487, A:P.488, A:I.490, A:V.498 Hydrogen bonds: A:F.317, A:Y.406, A:S.482, A:V.484, A:H.486, A:I.501, A:D.503, A:D.503, A:D.503, A:L.505, A:L.505, A:K.515, A:S.516, A:S.516, A:Y.565, A:K.569, A:K.569, A:C.588 Water bridges: A:Q.430, A:S.514, A:C.588, A:Y.680 Salt bridges: A:K.569 pi-Stacking: A:Y.565

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

NA.4: 2 residues within 4Å: Chain A: C.595, N.598 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:C.595 Water bridges: A:G.632

1 x QSH: 3,5-bis(bromanyl)-4-oxidanyl-benzoic acid(Non-covalent)

QSH.5: 11 residues within 4Å: Chain A: F.318, P.338, A.446, S.449, Y.453, N.479, K.515, R.579 Ligands: B12.3, QSB.6, BR.7 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:F.318 Hydrogen bonds: A:S.449, A:N.479, A:K.515, A:R.579, A:R.579 pi-Stacking: A:Y.453

1 x QSB: 3 bromo 4 hydroxybenzoic acid(Non-covalent)

QSB.6: 12 residues within 4Å: Chain A: F.337, P.338, A.446, S.449, Y.453, N.479, K.515, R.579, A.587 Ligands: B12.3, QSH.5, BR.7 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:F.337, A:P.338, A:Y.453 Hydrogen bonds: A:S.449, A:N.479, A:K.515, A:R.579, A:R.579

1 x BR: BROMIDE ION(Non-covalent)

BR.7: 6 residues within 4Å: Chain A: Y.453, K.515, R.579 Ligands: B12.3, QSH.5, QSB.6 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
C

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

Related Entries With Identical Sequence