SMTL ID : 6i3q.1 (2 other biounits)

The structure of thiocyanate dehydrogenase from Thioalkalivibrio paradoxus complex with acetate ions.

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.45 Å

Oligo State

homo-dimer

Ligands

4 x CU: COPPER (II) ION(Non-covalent)

CU.1: 5 residues within 4Å: Chain A: H.206, D.314, H.381 Ligands: ACT.3, ACT.4 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.206, A:D.314, A:D.314, A:H.381, H2O.3 CU.2: 6 residues within 4Å: Chain A: K.103, H.135, H.136, E.288, H.528 Ligands: ACT.4 5 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions, 1 Ligand-Ligand interactions Metal complexes: A:H.135, A:H.528, H2O.1, H2O.5, ACT.4 CU.5: 5 residues within 4Å: Chain B: H.206, D.314, H.381 Ligands: ACT.7, ACT.8 5 PLIP interactions: 3 interactions with chain B, 1 Ligand-Ligand interactions, 1 Ligand-Water interactions Metal complexes: B:H.206, B:D.314, B:H.381, ACT.7, H2O.19 CU.6: 5 residues within 4Å: Chain B: K.103, H.135, H.136, H.528 Ligands: ACT.8 4 PLIP interactions: 2 interactions with chain B, 1 Ligand-Ligand interactions, 1 Ligand-Water interactions Metal complexes: B:H.135, B:H.528, ACT.8, H2O.20

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

ACT.3: 8 residues within 4Å: Chain A: H.136, H.206, E.288, D.314, H.381, H.437 Ligands: CU.1, ACT.4 4 PLIP interactions: 4 interactions with chain A Salt bridges: A:H.136, A:H.206, A:H.381, A:H.437 ACT.4: 11 residues within 4Å: Chain A: H.135, H.136, V.205, H.206, E.288, D.314, H.381, H.528 Ligands: CU.1, CU.2, ACT.3 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:V.205 Water bridges: A:K.103 Salt bridges: A:K.103, A:H.135, A:H.136, A:H.528 ACT.7: 8 residues within 4Å: Chain B: H.136, H.206, D.314, H.381, H.437 Ligands: CU.5, ACT.8, GOL.10 4 PLIP interactions: 4 interactions with chain B Salt bridges: B:H.136, B:H.206, B:H.381, B:H.437 ACT.8: 9 residues within 4Å: Chain B: H.135, H.136, H.206, D.314, H.381, H.528 Ligands: CU.5, CU.6, ACT.7 5 PLIP interactions: 5 interactions with chain B Water bridges: B:K.103 Salt bridges: B:K.103, B:H.135, B:H.136, B:H.528 ACT.9: 2 residues within 4Å: Chain B: F.242, D.243 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:D.243 Water bridges: B:F.242 Salt bridges: B:K.284, B:R.306

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.10: 7 residues within 4Å: Chain B: P.291, F.436, H.437, W.452, M.481, H.482 Ligands: ACT.7 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.450, B:T.450, B:H.482

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

PEG.11: 2 residues within 4Å: Chain B: N.410, T.416 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.410, B:T.416

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tikhonova, T.V. et al., Trinuclear copper biocatalytic center forms an active site of thiocyanate dehydrogenase. Proc.Natl.Acad.Sci.USA (2020)

Release Date

2018-11-28

Peptides

Uncharacterized protein: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
D

Uncharacterized protein

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