SMTL ID : 8q4h.1

a membrane-bound menaquinol:organohalide oxidoreductase complex RDH complex

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-2-mer

Ligands

2 x JYF: (~{Z})-1,2-bis(chloranyl)ethene(Non-covalent)

JYF.1: 9 residues within 4Å: Chain A: F.22, W.109, A.120, V.285, Y.289, R.348, W.423, P.429 Ligands: COB.2 No protein-ligand interaction detected (PLIP) JYF.6: 9 residues within 4Å: Chain B: F.22, W.109, A.120, V.285, Y.289, R.348, W.423, P.429 Ligands: COB.7 No protein-ligand interaction detected (PLIP)

2 x COB: CO-METHYLCOBALAMIN(Non-covalent)

COB.2: 43 residues within 4Å: Chain A: F.4, Y.6, Y.15, N.20, F.21, F.22, Y.204, V.285, Y.289, M.292, N.315, G.318, I.319, S.320, V.321, P.322, A.332, N.335, G.336, L.337, L.338, P.345, H.347, R.348, I.349, K.351, R.369, A.404, E.405, N.406, T.409, E.410, K.411, W.412, L.414, S.416, C.419, W.423, P.429, S.431, V.434 Ligands: JYF.1, SF4.4 34 PLIP interactions: 34 interactions with chain A, Hydrophobic interactions: A:F.4, A:F.4, A:Y.6, A:Y.15, A:F.22, A:F.22, A:P.322, A:A.332, A:L.337, A:L.337, A:N.406, A:T.409, A:K.411, A:K.411, A:V.434 Hydrogen bonds: A:N.20, A:F.21, A:Y.204, A:G.318, A:S.320, A:N.335, A:L.338, A:L.338, A:R.348, A:R.348, A:I.349, A:K.351, A:A.404, A:N.406, A:W.412, A:S.416 Water bridges: A:K.411 Salt bridges: A:K.411 pi-Cation interactions: A:K.411 COB.7: 42 residues within 4Å: Chain B: F.4, Y.6, Y.15, N.20, F.21, F.22, Y.204, V.285, Y.289, N.315, G.318, I.319, S.320, V.321, P.322, A.332, N.335, G.336, L.337, L.338, P.345, H.347, R.348, I.349, K.351, R.369, A.404, E.405, N.406, T.409, E.410, K.411, W.412, L.414, S.416, C.419, W.423, S.431, C.433, V.434 Ligands: JYF.6, SF4.9 35 PLIP interactions: 35 interactions with chain B, Hydrophobic interactions: B:F.4, B:Y.6, B:Y.15, B:F.22, B:F.22, B:N.315, B:P.322, B:A.332, B:L.337, B:L.337, B:N.406, B:T.409, B:K.411, B:K.411, B:V.434 Hydrogen bonds: B:N.20, B:Y.204, B:G.318, B:S.320, B:N.335, B:L.338, B:L.338, B:R.348, B:R.348, B:I.349, B:K.351, B:A.404, B:N.406, B:W.412, B:S.416, B:S.431, B:S.431 Water bridges: B:H.347 Salt bridges: B:K.411 pi-Cation interactions: B:K.411

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

SF4.3: 10 residues within 4Å: Chain A: R.334, N.335, F.371, C.372, C.375, K.376, K.377, C.378, C.437, W.439 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.372, A:C.375, A:C.378, A:C.437 SF4.4: 10 residues within 4Å: Chain A: C.382, P.383, L.414, C.419, W.423, C.430, S.431, N.432, C.433 Ligands: COB.2 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.382, A:C.419, A:C.430, A:C.433 SF4.8: 11 residues within 4Å: Chain B: R.334, N.335, F.371, C.372, C.375, K.376, K.377, C.378, C.437, S.438, W.439 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.372, B:C.375, B:C.378, B:C.437 SF4.9: 9 residues within 4Å: Chain B: C.382, P.383, C.419, W.423, C.430, S.431, N.432, C.433 Ligands: COB.7 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.382, B:C.419, B:C.430, B:C.433

2 x MQ7: MENAQUINONE-7(Non-covalent)

MQ7.5: 14 residues within 4Å: Chain A: S.438, W.439, K.441, H.447, A.450, R.451, T.454, L.459, A.463, R.464, F.466, D.467, F.470 Chain D: W.54 13 PLIP interactions: 12 interactions with chain A, 1 interactions with chain D Hydrophobic interactions: A:K.441, A:A.450, A:R.451, A:T.454, A:L.459, A:A.463, A:F.466, A:D.467, A:F.470, D:W.54 pi-Stacking: A:W.439, A:W.439 pi-Cation interactions: A:K.441 MQ7.10: 14 residues within 4Å: Chain B: S.438, W.439, K.441, H.447, A.450, R.451, T.454, L.459, A.463, R.464, F.466, D.467, F.470 Chain C: W.54 13 PLIP interactions: 12 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: B:A.450, B:R.451, B:T.454, B:L.459, B:A.463, B:F.466, B:D.467, B:F.470, C:W.54 Hydrogen bonds: B:K.441 pi-Stacking: B:W.439, B:W.439 pi-Cation interactions: B:K.441

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cimmino, L. et al., Structure of a membrane-bound menaquinol:organohalide oxidoreductase. Nat Commun (2023)

Release Date

2023-10-18

Peptides

Tetrachloroethene reductive dehalogenase: AB
Probable tetrachloroethene reductive dehalogenase membrane anchor protein: CD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Membrane

We predict this structure to be a membrane protein.
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Tetrachloroethene reductive dehalogenase

Probable tetrachloroethene reductive dehalogenase membrane anchor protein