SMTL ID : 5ma2.1

PCE reductive dehalogenase from S. multivorans in complex with 4-iodophenol

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.88 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: BVQ.3 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.339, A:C.372, A:C.383, A:C.386 SF4.13: 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 SF4.14: 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: BVQ.15 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.339, B:C.372, B:C.383, B:C.386

2 x BVQ: NORPSEUDO-B12(Non-covalent)

BVQ.3: 37 residues within 4Å: Chain A: I.22, 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 42 PLIP interactions: 41 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:L.306, 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:Q.276, A:S.277, A:M.292, A:G.293, A:G.293, 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.364 Water bridges: A:V.278, A:S.290, A:S.290, A:W.365, A:Y.369, A:Y.369 Salt bridges: A:K.362 pi-Stacking: A:F.38 Metal complexes: H2O.1 BVQ.15: 39 residues within 4Å: Chain B: I.22, 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, I.344, H.357, N.358, Q.359, K.362, Q.364, Y.369, C.372, L.373, W.376, Y.382, C.386, V.387 Ligands: SF4.14 37 PLIP interactions: 37 interactions with chain B, Hydrophobic interactions: B:T.36, B:A.37, B:F.38, B:F.38, B:F.38, B:N.272, B:L.306, B:Y.369, B:Y.369, B:Y.369, B:L.373, 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:G.293, B:G.293, 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.364, B:Y.369 Water bridges: B:V.278, B:W.365 Salt bridges: B:K.362 pi-Stacking: B:F.38

1 x BEN: BENZAMIDINE(Non-functional Binders)

BEN.4: 5 residues within 4Å: Chain A: T.39, P.41, F.44, E.189 Ligands: IOL.10 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:F.44 Hydrogen bonds: A:T.39 Water bridges: A:L.186, A:E.189

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 9 residues within 4Å: Chain A: F.38, F.44, W.56, F.57, N.101, Y.102, Y.106, L.186, E.189 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:W.56, A:N.101, A:Y.106 GOL.6: 5 residues within 4Å: Chain A: F.110, L.113, M.119, M.254 Chain B: F.111 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:F.110 Water bridges: A:L.113, A:T.120, A:T.120, B:T.97 GOL.7: 3 residues within 4Å: Chain A: E.330, P.348, R.349 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.349, A:R.349 Water bridges: A:G.347, A:W.365 GOL.8: 3 residues within 4Å: Chain A: R.349, T.350, F.351 2 PLIP interactions: 2 interactions with chain A Water bridges: A:R.349, A:F.351 GOL.16: 6 residues within 4Å: Chain B: W.56, F.57, N.101, Y.102, L.186, E.189 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Y.106, B:Y.106 GOL.17: 5 residues within 4Å: Chain A: F.111 Chain B: F.110, L.113, M.119, M.254 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:F.110 Water bridges: B:T.120, A:T.97

8 x IOL: 4-IODOPHENOL(Non-covalent)

IOL.9: 9 residues within 4Å: Chain A: F.38, W.56, W.96, Y.102, T.242, Y.246, R.305, W.376, Y.382 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:F.38, A:Y.102, A:T.242, A:Y.382 pi-Stacking: A:W.96, A:W.376, A:Y.382 IOL.10: 4 residues within 4Å: Chain A: V.34, P.41, E.189 Ligands: BEN.4 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:P.41 IOL.11: 5 residues within 4Å: Chain A: L.58, L.186, H.187 Chain B: L.124, P.127 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Halogen bonds: B:L.124 Hydrophobic interactions: A:L.186 IOL.18: 3 residues within 4Å: Chain B: V.34, P.41, E.189 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:V.34 IOL.19: 5 residues within 4Å: Chain B: F.44, F.45, P.55, H.187 Ligands: IOL.20 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:F.44, B:F.45, B:P.55 IOL.20: 6 residues within 4Å: Chain A: L.124, P.127 Chain B: L.58, L.186, H.187 Ligands: IOL.19 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:L.58, B:L.58, B:L.186 Hydrogen bonds: B:H.187 Halogen bonds: A:L.124 IOL.21: 9 residues within 4Å: Chain B: F.38, W.56, W.96, Y.102, Y.246, N.272, R.305, W.376, Y.382 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:F.38, B:Y.102, B:Y.246, B:W.376, B:W.376 Hydrogen bonds: B:N.272, B:R.305 pi-Stacking: B:W.96, B:Y.382 IOL.22: 1 residues within 4Å: Chain B: P.391 No protein-ligand interaction detected (PLIP)

2 x IOD: IODIDE ION(Non-functional Binders)

IOD.12: 4 residues within 4Å: Chain A: A.60, K.64, G.381, Y.382 Ligand excluded by PLIP IOD.23: 3 residues within 4Å: Chain B: A.60, K.64, Y.382 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kunze, C. et al., Cobamide-mediated enzymatic reductive dehalogenation via long-range electron transfer. Nat Commun (2017)

Release Date

2017-07-12

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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