SMTL ID : 8yu5.1

The structure of non-activated thiocyanate dehydrogenase mutant with the H447Q substitution from Pelomicrobium methylotrophicum (pmTcDH H447Q)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.45 Å

Oligo State

homo-dimer

Ligands

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

PEG.1: 4 residues within 4Å: Chain A: S.190, D.191, L.192, K.193 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.192, A:K.193

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

EDO.2: 5 residues within 4Å: Chain A: N.188, G.200, T.201, M.314, D.315 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.188, A:T.201, A:D.315 Water bridges: A:T.201 EDO.3: 5 residues within 4Å: Chain A: Y.68, D.70, N.119, Y.121, N.135 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.121, A:N.135 EDO.4: 4 residues within 4Å: Chain A: N.342, E.365, D.366, W.369 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.342, A:D.366, A:D.366 Water bridges: A:E.365 EDO.8: 6 residues within 4Å: Chain B: P.383, Y.429, E.479, D.480, R.482, C.483 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:C.483 Water bridges: B:T.477, B:D.480, B:D.480, B:D.480 EDO.9: 5 residues within 4Å: Chain B: P.261, R.262, P.328, D.329, R.482 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:P.328 EDO.10: 6 residues within 4Å: Chain B: N.188, G.200, T.201, K.313, M.314, D.315 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:N.188, B:T.201, B:T.201, B:D.315, B:D.315 Water bridges: B:T.201

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

CU.5: 3 residues within 4Å: Chain A: G.19, H.20, M.21 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.20, H2O.15 CU.6: 4 residues within 4Å: Chain A: K.44, H.76, H.77, H.469 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.76, A:H.469, H2O.5, H2O.9 CU.7: 3 residues within 4Å: Chain A: H.147, D.255, Q.323 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.147, A:D.255, A:D.255, H2O.3, H2O.5 CU.11: 3 residues within 4Å: Chain B: H.147, D.255, H.322 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:H.147, B:D.255, B:H.322, H2O.29, H2O.33 CU.12: 4 residues within 4Å: Chain B: K.44, H.76, Y.105, H.469 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:H.76, B:H.469, H2O.22, H2O.24

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.13: 4 residues within 4Å: Chain B: T.151, P.152, D.153, R.281 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Varfolomeeva, L.A. et al., The structure of non-activated thiocyanate dehydrogenase mutant with the H447Q substitution from Pelomicrobium methylotrophicum (pmTcDH H447Q). To Be Published

Release Date

2024-04-24

Peptides

Twin-arginine translocation signal domain-containing protein: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Twin-arginine translocation signal domain-containing protein

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