SMTL ID : 9h4t.1 (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: 35 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, MLT.13 34 PLIP interactions: 34 interactions with chain A Hydrogen bonds: A:W.160, A:R.377, A:G.484, A:N.486, A:H.489, A:Q.492, A:I.510, A:N.512, A:R.533, A:R.533, A:S.694, A:S.694, A:L.701, A:S.703, A:S.703, A:S.703, A:Q.704, A:Q.704, A:N.791 Water bridges: A:H.93, A:H.93, A:S.162, A:S.162, A:R.490, A:D.563, A:H.696 Salt bridges: A:H.489, A:H.489, A:R.490, A:D.511, A:D.563, A:H.702, A:H.702, A:E.769 PGD.2: 36 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 Ligands: PGD.1, 6MO.3 25 PLIP interactions: 25 interactions with chain A Hydrogen bonds: A:K.234, A:N.235, A:N.235, A:Q.237, 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 Water bridges: A:G.229, A:D.231, A:R.377, 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: 4 residues within 4Å: Chain A: S.191 Ligands: PGD.1, PGD.2, MLT.13 No protein-ligand interaction detected (PLIP)

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

PEG.4: 1 residues within 4Å: Ligands: PEG.22 No protein-ligand interaction detected (PLIP) PEG.5: 5 residues within 4Å: Chain A: S.49, E.51, V.66, K.67 Ligands: PEG.6 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.49 PEG.6: 3 residues within 4Å: Chain A: D.68 Ligands: PEG.5, PEG.20 No protein-ligand interaction detected (PLIP) PEG.7: 2 residues within 4Å: Chain A: Q.557, F.558 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.557 Water bridges: A:R.70, A:H.95, A:Q.557 PEG.8: 2 residues within 4Å: Chain A: W.672, E.674 No protein-ligand interaction detected (PLIP) PEG.9: 4 residues within 4Å: Chain A: K.346, R.678, H.680, G.681 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.346, A:R.678 PEG.17: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) PEG.18: 3 residues within 4Å: Chain A: S.183, G.185, S.447 2 PLIP interactions: 2 interactions with chain A Water bridges: A:A.174, A:S.183 PEG.19: 2 residues within 4Å: Chain A: H.114, L.115 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.114 PEG.20: 2 residues within 4Å: Chain A: D.68 Ligands: PEG.6 No protein-ligand interaction detected (PLIP) PEG.21: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) PEG.22: 2 residues within 4Å: Ligands: PEG.4, MLT.15 No protein-ligand interaction detected (PLIP)

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

PGE.10: 9 residues within 4Å: Chain A: A.97, R.99, I.100, R.101, Y.102, M.104, N.829, P.831, E.833 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.99, A:R.101, A:Y.102 PGE.11: 2 residues within 4Å: Chain A: D.123, R.125 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.125 PGE.12: 4 residues within 4Å: Chain A: K.67, D.68, R.70 Ligands: MLT.15 2 PLIP interactions: 2 interactions with chain A Water bridges: A:K.67, A:R.70

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

MLT.13: 7 residues within 4Å: Chain A: G.159, W.160, D.189, S.191, Y.209 Ligands: PGD.1, 6MO.3 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:D.189 Hydrogen bonds: A:S.191 Water bridges: A:W.160, A:Y.190, A:R.490 MLT.14: 6 residues within 4Å: Chain A: V.72, A.88, G.89, P.91, D.92, T.710 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:P.91 Hydrogen bonds: A:D.92 MLT.15: 2 residues within 4Å: Ligands: PGE.12, PEG.22 No protein-ligand interaction detected (PLIP) MLT.16: 3 residues within 4Å: Chain A: D.664, D.665, Q.801 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.664, A:Q.801 Water bridges: A:D.665, A:D.665, A:Q.801

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
A

Trimethylamine-N-oxide reductase 1

Related Entries With Identical Sequence