SMTL ID : 5oex.1 (2 other biounits)

Complex with iodine ion for thiocyanate dehydrogenase from Thioalkalivibrio paradoxus

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-tetramer

Ligands

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

CU.1: 3 residues within 4Å: Chain A: H.125, D.233, H.300 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.125, A:D.233, A:H.300, H2O.3, H2O.8 CU.2: 5 residues within 4Å: Chain A: K.22, H.54, H.447 Ligands: CU.3, IOD.8 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.54, A:H.447, H2O.2 CU.3: 6 residues within 4Å: Chain A: K.22, H.54, H.55, H.447 Ligands: CU.2, IOD.8 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.54, A:H.447, H2O.2, H2O.3 CU.4: 4 residues within 4Å: Chain A: H.356, H.401, H.447 Ligands: IOD.8 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.356, A:H.401, H2O.8 CU.9: 3 residues within 4Å: Chain B: H.125, D.233, H.300 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:H.125, B:D.233, B:D.233, B:H.300 CU.10: 4 residues within 4Å: Chain B: K.22, H.54, H.447 Ligands: CU.11 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.54, B:H.447, H2O.14 CU.11: 5 residues within 4Å: Chain B: K.22, H.54, H.55, H.447 Ligands: CU.10 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:H.54, B:H.447, H2O.14, H2O.14 CU.16: 3 residues within 4Å: Chain C: H.125, D.233, H.300 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:H.125, C:D.233, C:H.300, H2O.22, H2O.26 CU.17: 6 residues within 4Å: Chain C: K.22, H.54, H.55, H.447 Ligands: CU.18, IOD.21 4 PLIP interactions: 2 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:H.54, C:H.447, H2O.21, H2O.23 CU.18: 5 residues within 4Å: Chain C: K.22, H.54, H.447 Ligands: CU.17, IOD.21 3 PLIP interactions: 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:H.54, C:H.447, H2O.23 CU.19: 4 residues within 4Å: Chain C: H.356, H.401, H.447 Ligands: IOD.21 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:H.356, C:H.401 CU.22: 3 residues within 4Å: Chain D: H.125, D.233, H.300 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:H.125, D:D.233, D:D.233, D:H.300 CU.23: 4 residues within 4Å: Chain D: H.356, H.401, H.447 Ligands: IOD.28 3 PLIP interactions: 2 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:H.356, D:H.401, H2O.35 CU.24: 5 residues within 4Å: Chain D: K.22, H.54, H.447 Ligands: CU.25, IOD.28 3 PLIP interactions: 2 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:H.54, D:H.447, H2O.28 CU.25: 6 residues within 4Å: Chain D: K.22, H.54, H.55, H.447 Ligands: CU.24, IOD.28 4 PLIP interactions: 2 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:H.54, D:H.447, H2O.28, H2O.29

1 x P4G: 1-ETHOXY-2-(2-ETHOXYETHOXY)ETHANE(Non-covalent)

P4G.5: 2 residues within 4Å: Chain A: D.133, R.156 No protein-ligand interaction detected (PLIP)

8 x IOD: IODIDE ION(Non-functional Binders)

IOD.6: 4 residues within 4Å: Chain A: R.193, Q.197 Chain C: R.193, Q.197 Ligand excluded by PLIP IOD.7: 4 residues within 4Å: Chain A: W.206, V.209, G.212, A.215 Ligand excluded by PLIP IOD.8: 7 residues within 4Å: Chain A: H.55, H.356, H.401, H.447 Ligands: CU.2, CU.3, CU.4 Ligand excluded by PLIP IOD.20: 4 residues within 4Å: Chain C: W.206, V.209, G.212, A.215 Ligand excluded by PLIP IOD.21: 7 residues within 4Å: Chain C: H.55, H.356, H.401, H.447 Ligands: CU.17, CU.18, CU.19 Ligand excluded by PLIP IOD.26: 4 residues within 4Å: Chain D: W.206, V.209, G.212, A.215 Ligand excluded by PLIP IOD.27: 1 residues within 4Å: Chain D: Y.83 Ligand excluded by PLIP IOD.28: 7 residues within 4Å: Chain D: H.55, H.356, H.401, H.447 Ligands: CU.23, CU.24, CU.25 Ligand excluded by PLIP

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

EDO.12: 5 residues within 4Å: Chain B: K.14, D.31, S.33, T.34, Y.65 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.31, B:S.33 Water bridges: B:D.31 EDO.13: 6 residues within 4Å: Chain B: W.206, L.208, V.209, G.212, A.215, V.221 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:V.209 EDO.14: 6 residues within 4Å: Chain B: P.60, E.67, F.68, E.69, K.102, R.150 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:P.60, B:K.102, B:R.150 Water bridges: B:R.150

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.15: 8 residues within 4Å: Chain B: M.370, W.372, P.377, N.378, G.379, E.393, V.394, D.395 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:M.370, B:G.379, B:V.394 Water bridges: B:E.393

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tikhonova, T.V. et al., Discovery and characterization of a novel copper containing enzyme - THIOCYANATE DEHYDROGENASE. To Be Published

Release Date

2018-08-01

Peptides

THIOCYANATE DEHYDROGENASE: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

THIOCYANATE DEHYDROGENASE

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