SMTL ID : 9h4t.2 (1 other biounit)

Crystal Structure of TorA

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.86 Å

Oligo State

monomer

Ligands

2 x PGD: 2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,7,8A,9-TETRAHYDRO-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-4-ONE GUANOSINE DINUCLEOTIDE(Non-covalent)

PGD.1: 34 residues within 4Å: Chain A: G.159, W.160, Q.161, S.162, A.169, Y.190, S.191, R.377, G.484, T.485, N.486, H.489, R.490, Q.492, I.510, D.511, N.512, T.515, A.527, R.533, D.563, S.694, H.696, L.701, H.702, S.703, Q.704, E.769, N.791, T.794, A.808, H.809 Ligands: PGD.2, 6MO.3 30 PLIP interactions: 30 interactions with chain A Hydrogen bonds: A:W.160, A:R.377, A:G.484, A:N.486, A:R.490, A:I.510, A:N.512, A:R.533, A:R.533, A:S.694, A:L.701, A:S.703, A:Q.704, A:Q.704, A:N.791, A:N.791 Water bridges: A:S.162, A:T.485, A:T.485, A:T.485, A:R.490, A:R.490, A:T.515, A:D.563 Salt bridges: A:H.489, A:R.490, A:D.563, A:H.702, A:H.702, A:E.769 PGD.2: 37 residues within 4Å: Chain A: M.86, W.160, S.191, W.228, G.229, S.230, K.234, N.235, Q.237, A.238, I.268, D.269, P.270, V.271, T.273, V.289, P.291, Q.292, D.294, G.372, W.373, C.374, V.375, R.377, M.378, H.410, Q.693, V.695, H.696, P.697, R.700, L.701, H.702, R.766, E.769 Ligands: PGD.1, 6MO.3 24 PLIP interactions: 24 interactions with chain A Hydrogen bonds: A:K.234, A:N.235, A:N.235, A:I.268, A:Q.292, A:W.373, A:C.374, A:Q.693, A:Q.693, A:H.696, A:H.696, A:H.702, A:R.766, A:E.769 Water bridges: A:D.231, A:D.231, A:H.410 Salt bridges: A:K.234, A:D.269, A:D.294, A:R.377, A:H.410, A:H.696, A:H.696

1 x 6MO: MOLYBDENUM(VI) ION(Covalent)

6MO.3: 3 residues within 4Å: Chain A: S.191 Ligands: PGD.1, PGD.2 No protein-ligand interaction detected (PLIP)

3 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.4: 2 residues within 4Å: Chain A: R.101 Ligands: MLT.8 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.101 Water bridges: A:R.101 PEG.11: 1 residues within 4Å: Chain A: S.648 No protein-ligand interaction detected (PLIP) PEG.12: 2 residues within 4Å: Chain A: Q.337, W.343 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.337

2 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.5: 3 residues within 4Å: Chain A: P.200, G.204, G.645 1 PLIP interactions: 1 interactions with chain A Water bridges: A:M.206 PGE.7: 5 residues within 4Å: Chain A: Y.306, Y.311, K.313, A.317, F.323 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.311, A:K.313

1 x 1PE: PENTAETHYLENE GLYCOL(Non-functional Binders)

1PE.6: 5 residues within 4Å: Chain A: Q.325, P.328, K.334, Y.654, H.669 4 PLIP interactions: 4 interactions with chain A Water bridges: A:Q.325, A:Q.325, A:Y.654, A:K.656

3 x MLT: D-MALATE(Non-covalent)(Non-functional Binders)

MLT.8: 7 residues within 4Å: Chain A: R.99, R.101, Y.102, M.104, P.831, E.833 Ligands: PEG.4 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.101, A:R.101, A:E.833, A:E.833 Water bridges: A:A.97 MLT.9: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MLT.10: 1 residues within 4Å: Chain A: R.128 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:R.128 Hydrogen bonds: A:E.133 Water bridges: A:R.128 Salt bridges: A:R.128

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Panwar, A. et al., Purification and Electron Transfer from Soluble c-Type Cytochrome TorC to TorA for Trimethylamine N-Oxide Reduction. Int J Mol Sci (2024)

Release Date

2025-02-26

Peptides

Trimethylamine-N-oxide reductase 1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

Trimethylamine-N-oxide reductase 1

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