SMTL ID : 8qfq.1

Ergothioneine dioxygenase, variant H147A, from Thermocatellispora tengchongensis in complex with manganese

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-dimer

Ligands

2 x MN: MANGANESE (II) ION(Non-covalent)

MN.1: 5 residues within 4Å: Chain A: H.88, H.90, H.134 Ligands: ACT.3, ACT.4 6 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions, 2 Ligand-Ligand interactions Metal complexes: A:H.88, A:H.90, A:H.134, H2O.1, ACT.3, ACT.4 MN.5: 5 residues within 4Å: Chain B: H.88, H.90, H.134 Ligands: ACT.6, ACT.7 6 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions, 2 Ligand-Ligand interactions Metal complexes: B:H.88, B:H.90, B:H.134, H2O.3, ACT.6, ACT.7

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

PGE.2: 5 residues within 4Å: Chain A: W.87, P.109, I.133, Y.159, M.167 No protein-ligand interaction detected (PLIP)

5 x ACT: ACETATE ION(Non-functional Binders)

ACT.3: 11 residues within 4Å: Chain A: H.88, H.90, A.96, V.97, F.128, H.134, L.136, A.147, Y.149 Ligands: MN.1, ACT.4 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:V.97, A:F.128, A:A.147, A:Y.149 Hydrogen bonds: A:Y.149 Salt bridges: A:H.88, A:H.90, A:H.134 ACT.4: 10 residues within 4Å: Chain A: R.61, T.85, H.88, H.90, Y.149, L.153, L.156, Y.174 Ligands: MN.1, ACT.3 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:L.153 Hydrogen bonds: A:R.61, A:Y.149 Salt bridges: A:H.88, A:H.90 ACT.6: 10 residues within 4Å: Chain B: H.90, A.96, V.97, F.128, H.134, L.136, A.147, Y.149 Ligands: MN.5, ACT.7 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:V.97, B:F.128, B:A.147, B:Y.149 Hydrogen bonds: B:Y.149 Water bridges: B:Y.149 Salt bridges: B:H.88, B:H.90, B:H.134 ACT.7: 8 residues within 4Å: Chain B: H.88, H.90, H.134, Y.149, L.153, L.156 Ligands: MN.5, ACT.6 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:L.153, B:L.156 Hydrogen bonds: B:Y.149 Water bridges: B:Y.63 Salt bridges: B:H.88, B:H.90, B:H.134 ACT.8: 7 residues within 4Å: Chain A: S.121, E.122, E.124 Chain B: R.32, R.36, F.126, S.127 7 PLIP interactions: 4 interactions with chain A, 3 interactions with chain B Water bridges: A:S.121, A:S.121, A:S.121, A:S.121 Hydrogen bonds: B:S.127 Salt bridges: B:R.32, B:R.36

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

EDO.9: 3 residues within 4Å: Chain B: R.28, R.33, E.34 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.33, B:R.33, B:E.34, B:E.34 EDO.10: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

1 x MG: MAGNESIUM ION(Non-covalent)

MG.11: 3 residues within 4Å: Chain B: E.22, H.67, D.69 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.22, B:H.67, B:D.69, H2O.4

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nalivaiko, E.Y. et al., Enzyme-Catalyzed Oxidative Degradation of Ergothioneine. Angew.Chem.Int.Ed.Engl. (2024)

Release Date

2023-12-27

Peptides

Cysteine dioxygenase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Cysteine dioxygenase