SMTL ID : 6uwe.2 (1 other biounit)

Crystal structure of recombinant thiocyanate dehydrogenase from Thioalkalivibrio paradoxus saturated with copper

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-dimer

Ligands

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

CU.1: 5 residues within 4Å: Chain A: H.129, D.237, H.304, Q.305 Ligands: CU.4 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.129, A:D.237, A:D.237, A:H.304 CU.2: 7 residues within 4Å: Chain A: K.26, H.58, H.59, H.451 Ligands: CU.4, UNX.7, UNX.8 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.58, A:H.451, H2O.9 CU.3: 6 residues within 4Å: Chain A: F.359, H.360, H.405, H.451 Ligands: UNX.7, UNX.8 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:H.360, A:H.405 CU.4: 8 residues within 4Å: Chain A: H.58, H.59, V.128, H.129 Ligands: CU.1, CU.2, UNX.7, UNX.8 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.59, H2O.7 CU.5: 1 residues within 4Å: Chain A: H.334 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:H.334, H2O.1, H2O.6, H2O.19 CU.6: 1 residues within 4Å: Chain A: H.232 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:H.232, H2O.10, H2O.16, H2O.18 CU.9: 5 residues within 4Å: Chain B: H.129, D.237, H.304, Q.305 Ligands: CU.12 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:H.129, B:D.237, B:D.237, B:H.304 CU.10: 6 residues within 4Å: Chain B: K.26, H.58, H.59, H.451 Ligands: CU.12, UNX.15 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.58, B:H.451, H2O.26 CU.11: 5 residues within 4Å: Chain B: F.359, H.360, H.405, H.451 Ligands: UNX.15 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:H.360, B:H.405 CU.12: 7 residues within 4Å: Chain B: H.58, H.59, V.128, H.129 Ligands: CU.9, CU.10, UNX.15 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.59, H2O.33 CU.13: 1 residues within 4Å: Chain B: H.334 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:H.334, H2O.24, H2O.34 CU.14: 1 residues within 4Å: Chain B: H.232 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:H.232, H2O.38, H2O.41

3 x UNX: UNKNOWN ATOM OR ION(Non-functional Binders)

UNX.7: 7 residues within 4Å: Chain A: H.58, H.59, H.451 Ligands: CU.2, CU.3, CU.4, UNX.8 No protein-ligand interaction detected (PLIP) UNX.8: 9 residues within 4Å: Chain A: H.304, Q.305, F.359, H.360, H.405 Ligands: CU.2, CU.3, CU.4, UNX.7 No protein-ligand interaction detected (PLIP) UNX.15: 5 residues within 4Å: Chain B: H.59, H.451 Ligands: CU.10, CU.11, CU.12 No protein-ligand interaction detected (PLIP)

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

2019-11-27

Peptides

thiocyanate dehydrogenase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
C

thiocyanate dehydrogenase

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