SMTL ID : 6g50.3 (2 other biounits)

The structure of thiocyanate dehydrogenase from Thioalkalivibrio paradoxus as isolated.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.65 Å

Oligo State

homo-dimer

Ligands

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

CU.1: 3 residues within 4Å: Chain A: H.125, H.356 Ligands: SO4.5 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.125, H2O.12 CU.2: 5 residues within 4Å: Chain A: K.22, H.54, H.55, H.447 Ligands: SO4.5 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.54, A:H.447, H2O.3 CU.3: 4 residues within 4Å: Chain A: R.100, R.112, R.150, E.151 No protein-ligand interaction detected (PLIP) CU.4: 6 residues within 4Å: Chain A: H.300, N.315, S.316, N.320, N.353, T.354 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:N.315, A:S.316, A:T.354 CU.6: 4 residues within 4Å: Chain B: H.125, D.233, H.300 Ligands: SO4.11 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.125, B:D.233, B:D.233, B:H.300, H2O.15 CU.7: 5 residues within 4Å: Chain B: N.315, S.316, N.320, N.353, T.354 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:N.315, B:S.316, B:T.354, H2O.17 CU.8: 3 residues within 4Å: Chain B: Q.6, D.7, D.10 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:D.7, B:D.10

5 x SO4: SULFATE ION(Non-functional Binders)

SO4.5: 10 residues within 4Å: Chain A: H.54, H.55, V.124, H.125, F.355, H.356, H.401, H.447 Ligands: CU.1, CU.2 8 PLIP interactions: 8 interactions with chain A Water bridges: A:K.22, A:R.249, A:R.249 Salt bridges: A:H.54, A:H.55, A:H.125, A:H.356, A:H.447 SO4.9: 1 residues within 4Å: Chain B: R.318 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:R.318 SO4.10: 4 residues within 4Å: Chain B: K.102, Q.111 Ligands: EDO.13, EDO.14 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:Q.111 Water bridges: B:K.102, B:K.102, B:K.102 Salt bridges: B:K.102 SO4.11: 7 residues within 4Å: Chain B: H.54, H.55, H.300, H.356, H.401, H.447 Ligands: CU.6 6 PLIP interactions: 6 interactions with chain B Water bridges: B:K.22, B:K.22 Salt bridges: B:H.55, B:H.356, B:H.401, B:H.447 SO4.12: 6 residues within 4Å: Chain B: G.47, D.48, T.49, C.50, G.93, K.97 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:D.48, B:T.49, B:C.50 Water bridges: B:T.49, B:E.94, B:G.95 Salt bridges: B:K.97

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

EDO.13: 3 residues within 4Å: Chain B: R.112 Ligands: SO4.10, EDO.14 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.112, B:R.112 Water bridges: B:Q.111 EDO.14: 8 residues within 4Å: Chain B: E.69, R.100, Q.111, R.112, R.150, D.153 Ligands: SO4.10, EDO.13 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.112, B:D.153 Water bridges: B:E.69, B:K.102

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

2019-04-10

Peptides

Uncharacterized protein: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
C

Uncharacterized protein

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