SMTL ID : 5obp.1

PCE reductive dehalogenase from S. multivorans with 6-hydroxybenzimidazolyl norcobamide cofactor

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.59 Å

Oligo State

homo-dimer

Ligands

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

SF4.1: 13 residues within 4Å: Chain A: S.290, R.291, M.292, I.296, C.329, C.332, K.333, K.334, C.335, C.390, P.391, F.392, F.412 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.329, A:C.332, A:C.335, A:C.390 SF4.2: 10 residues within 4Å: Chain A: C.339, P.340, S.341, I.344, C.372, C.383, G.384, V.385, C.386 Ligands: 9QQ.3 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.339, A:C.372, A:C.383, A:C.386 SF4.8: 13 residues within 4Å: Chain B: S.290, R.291, M.292, I.296, F.328, C.329, C.332, K.333, K.334, C.335, C.390, P.391, F.392 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.329, B:C.332, B:C.335, B:C.390 SF4.9: 10 residues within 4Å: Chain B: C.339, P.340, S.341, I.344, C.372, C.383, G.384, V.385, C.386 Ligands: 9QQ.10 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.339, B:C.372, B:C.383, B:C.386

2 x 9QQ: 6-hydroxybenzimidazolyl-norcobamide(Non-covalent)

9QQ.3: 36 residues within 4Å: Chain A: Y.31, T.36, A.37, F.38, Y.170, T.242, Y.246, M.249, N.272, G.275, Q.276, S.277, V.278, A.279, A.289, M.292, G.293, A.294, C.295, P.302, V.304, R.305, L.306, K.308, H.357, N.358, Q.359, K.362, Q.364, Y.369, C.372, W.376, Y.382, C.386, V.387 Ligands: SF4.2 41 PLIP interactions: 40 interactions with chain A, 1 Ligand-Water interactions Hydrophobic interactions: A:T.36, A:A.37, A:F.38, A:F.38, A:F.38, A:N.272, A:A.289, A:L.306, A:K.362, A:Y.369, A:Y.369, A:Y.369, A:V.387 Hydrogen bonds: A:Y.31, A:A.37, A:Y.170, A:T.242, A:T.242, A:N.272, A:G.275, A:S.277, A:M.292, A:C.295, A:C.295, A:R.305, A:R.305, A:L.306, A:K.308, A:H.357, A:N.358, A:Q.359, A:Q.359, A:Q.364, A:Y.369, A:Y.369 Water bridges: A:V.278, A:W.365, A:Y.382 Salt bridges: A:K.362 pi-Stacking: A:F.38 Metal complexes: H2O.13 9QQ.10: 36 residues within 4Å: Chain B: Y.31, T.36, A.37, F.38, Y.170, T.242, Y.246, M.249, N.272, G.275, Q.276, S.277, V.278, A.279, A.289, M.292, G.293, A.294, C.295, P.302, V.304, R.305, L.306, K.308, H.357, N.358, Q.359, K.362, Q.364, Y.369, C.372, W.376, Y.382, C.386, V.387 Ligands: SF4.9 40 PLIP interactions: 39 interactions with chain B, 1 Ligand-Water interactions Hydrophobic interactions: B:T.36, B:A.37, B:F.38, B:F.38, B:F.38, B:N.272, B:A.289, B:K.362, B:Y.369, B:Y.369, B:Y.369, B:V.387 Hydrogen bonds: B:A.37, B:Y.170, B:T.242, B:T.242, B:N.272, B:G.275, B:S.277, B:M.292, B:C.295, B:C.295, B:R.305, B:R.305, B:L.306, B:K.308, B:H.357, B:N.358, B:Q.359, B:Q.359, B:Q.364 Water bridges: B:V.278, B:Q.364, B:W.365, B:W.365, B:N.367, B:Y.369 Salt bridges: B:K.362 pi-Stacking: B:F.38 Metal complexes: H2O.30

1 x BEN: BENZAMIDINE(Non-functional Binders)

BEN.4: 5 residues within 4Å: Chain A: T.39, P.41, F.44, F.45, E.189 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:P.41, A:F.44, A:F.45, A:F.45 Hydrogen bonds: A:T.39, A:L.186

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 5 residues within 4Å: Chain A: F.110, L.113, M.119, M.254 Chain B: F.111 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:F.110 Water bridges: A:L.113, A:T.120, A:T.120, A:T.120, A:T.120 GOL.6: 3 residues within 4Å: Chain A: E.330, P.348, R.349 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.349, A:R.349 Water bridges: A:E.327, A:E.327, A:G.347, A:W.365 GOL.7: 3 residues within 4Å: Chain A: D.322, G.324, E.327 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.322 Water bridges: A:F.323, A:G.324 GOL.11: 6 residues within 4Å: Chain A: L.98, F.111 Chain B: F.110, L.113, M.119, M.254 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:F.110, B:T.120 Water bridges: B:T.120, B:T.120

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Keller, S. et al., Selective Utilization of Benzimidazolyl-Norcobamides as Cofactors by the Tetrachloroethene Reductive Dehalogenase of Sulfurospirillum multivorans. J. Bacteriol. (2018)

Release Date

2018-02-14

Peptides

Tetrachloroethene reductive dehalogenase catalytically active subunit: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Tetrachloroethene reductive dehalogenase catalytically active subunit

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