SMTL ID : 6ktv.1

The structure of EanB complex with hercynine and persulfided Cys412

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

monomer

Ligands

1 x AVJ: N,N,N-trimethyl-histidine(Non-covalent)

AVJ.1: 12 residues within 4Å: Chain A: Y.191, E.214, W.219, G.259, Y.356, Y.358, A.377, Y.378, C.415, T.417, W.419, R.420 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:W.419 Hydrogen bonds: A:G.259, A:Y.378, A:T.417 Salt bridges: A:E.214 pi-Cation interactions: A:Y.191, A:W.219

1 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 6 residues within 4Å: Chain A: W.219, N.220, R.269, T.417, D.440, G.441 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:W.219, A:T.417, A:D.440, A:D.440, H2O.5

8 x CL: CHLORIDE ION(Non-functional Binders)

CL.3: 5 residues within 4Å: Chain A: C.342, R.344, R.364, I.365, Y.414 Ligand excluded by PLIP CL.4: 6 residues within 4Å: Chain A: F.248, A.262, G.263, H.264, I.265, R.384 Ligand excluded by PLIP CL.5: 4 residues within 4Å: Chain A: E.156, Q.157, Y.158, N.159 Ligand excluded by PLIP CL.6: 2 residues within 4Å: Chain A: S.50, V.53 Ligand excluded by PLIP CL.7: 3 residues within 4Å: Chain A: D.255, E.256, F.257 Ligand excluded by PLIP CL.8: 1 residues within 4Å: Chain A: N.193 Ligand excluded by PLIP CL.9: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.10: 4 residues within 4Å: Chain A: W.433, P.434, R.435, V.436 Ligand excluded by PLIP

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.11: 6 residues within 4Å: Chain A: H.379, E.381, R.384, N.385, H.386, H.388 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.384 Water bridges: A:M.380, A:N.385 GOL.12: 6 residues within 4Å: Chain A: R.59, S.60, M.69, R.70, Y.114, E.165 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.60, A:R.70, A:R.70 GOL.13: 8 residues within 4Å: Chain A: W.88, I.97, F.100, K.101, N.385, R.391, E.395 Ligands: IMD.32 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.101, A:E.395 Water bridges: A:E.381, A:N.385, A:E.392

11 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.14: 7 residues within 4Å: Chain A: R.154, L.155, E.156, Y.393, E.397, M.431 Ligands: IMD.30 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.154, A:E.156, A:E.397 EDO.15: 3 residues within 4Å: Chain A: R.221, R.222, T.223 2 PLIP interactions: 2 interactions with chain A Water bridges: A:R.221, A:Y.276 EDO.16: 3 residues within 4Å: Chain A: N.168, F.297, A.298 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:A.298 EDO.17: 2 residues within 4Å: Chain A: T.183, F.184 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:F.184 Water bridges: A:F.184 EDO.18: 5 residues within 4Å: Chain A: E.328, M.332, S.338, H.410 Ligands: PDO.28 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.328, A:E.328, A:S.338, A:S.338 EDO.19: 3 residues within 4Å: Chain A: I.350, T.456, G.457 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.456, A:T.456 EDO.20: 2 residues within 4Å: Chain A: D.339, G.367 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.339 EDO.21: 5 residues within 4Å: Chain A: E.372, N.382, Y.383, R.391, I.399 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.391 Water bridges: A:E.372, A:R.391 EDO.22: 5 residues within 4Å: Chain A: K.330, L.333, Q.334, W.446, P.453 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.330 EDO.23: 4 residues within 4Å: Chain A: A.323, V.324, D.325, E.328 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.325 Water bridges: A:R.221, A:D.325, A:E.328 EDO.24: 4 residues within 4Å: Chain A: D.62, K.87, S.291, T.389 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.62, A:K.87, A:S.291 Water bridges: A:A.61

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

PEG.25: 6 residues within 4Å: Chain A: N.159, R.160, E.178, E.280, D.281, R.283 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.160, A:E.280, A:R.283

1 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.26: 1 residues within 4Å: Chain A: Y.34 1 PLIP interactions: 1 interactions with chain A Water bridges: A:Q.121

3 x PDO: 1,3-PROPANDIOL(Non-covalent)

PDO.27: 4 residues within 4Å: Chain A: R.160, M.275, R.319, L.429 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.280, A:R.319 PDO.28: 5 residues within 4Å: Chain A: E.321, H.410, R.435, S.437 Ligands: EDO.18 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.437, A:S.437 PDO.29: 2 residues within 4Å: Chain A: E.51, K.52 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.51, A:E.51, A:K.52

3 x IMD: IMIDAZOLE(Non-covalent)

IMD.30: 5 residues within 4Å: Chain A: E.156, P.407, M.431, G.432 Ligands: EDO.14 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.156 IMD.31: 4 residues within 4Å: Chain A: N.181, D.182, T.183, S.239 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.183 IMD.32: 5 residues within 4Å: Chain A: N.96, I.97, F.100, H.386 Ligands: GOL.13 2 PLIP interactions: 2 interactions with chain A Water bridges: A:E.381 pi-Stacking: A:H.386

1 x NI: NICKEL (II) ION(Non-covalent)

NI.33: 5 residues within 4Å: Chain A: M.332, L.333, S.335, S.338, D.339 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cheng, R. et al., Single-Step Replacement of an Unreactive C-H Bond by a C-S Bond Using Polysulfide as the Direct Sulfur Source in the Anaerobic Ergothioneine Biosynthesis. Acs Catalysis (2020)

Release Date

2020-08-26

Peptides

Sulfurtransferase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Sulfurtransferase

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