SMTL ID : 6t7j.2 (1 other biounit)

As-isolated Ni-free crystal structure of carbon monoxide dehydrogenase from Thermococcus sp. AM4 produced without CooC maturase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.43 Å

Oligo State

homo-dimer

Ligands

2 x SF4: IRON/SULFUR CLUSTER(Non-covalent)

SF4.1: 10 residues within 4Å: Chain A: C.55, N.57, C.58, M.60, G.61, C.63, V.76, C.77, R.87, I.206 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.55, A:C.58, A:C.63, A:C.77 SF4.6: 12 residues within 4Å: Chain B: C.55, R.56, N.57, C.58, M.60, G.61, C.63, G.75, V.76, C.77, R.87, I.206 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.55, B:C.58, B:C.63, B:C.77

2 x FES: FE2/S2 (INORGANIC) CLUSTER(Non-covalent)

FES.2: 5 residues within 4Å: Chain A: C.46, G.49, C.54 Chain B: R.56 Ligands: FES.7 2 PLIP interactions: 2 interactions with chain A, Metal complexes: A:C.46, A:C.54 FES.7: 7 residues within 4Å: Chain A: C.54, R.56 Chain B: C.46, C.54, R.56, R.64 Ligands: FES.2 2 PLIP interactions: 2 interactions with chain B, Metal complexes: B:C.46, B:C.54

2 x MSK: Broken Fe4S4 cluster(Non-covalent)

MSK.3: 12 residues within 4Å: Chain A: H.269, C.304, C.305, F.322, C.343, G.450, C.451, C.481, C.522, M.556, S.557, K.559 5 PLIP interactions: 5 interactions with chain A, Metal complexes: A:H.269, A:C.305, A:C.343, A:C.451, A:C.481 MSK.8: 12 residues within 4Å: Chain B: H.269, C.304, C.305, F.322, C.343, G.450, C.451, C.481, C.522, M.556, S.557, K.559 6 PLIP interactions: 5 interactions with chain B, 1 Ligand-Ligand interactions Metal complexes: B:H.269, B:C.305, B:C.343, B:C.451, B:C.481, MSK.8

3 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.4: 2 residues within 4Å: Chain A: K.408, H.409 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:K.408, A:H.409 PO4.9: 4 residues within 4Å: Chain B: G.187, R.203, S.214, R.221 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.214 Water bridges: B:R.203 Salt bridges: B:R.203, B:R.221 PO4.10: 3 residues within 4Å: Chain B: K.18, E.22, H.409 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.22 Salt bridges: B:K.18, B:H.409

1 x CIT: CITRIC ACID(Non-functional Binders)

CIT.5: 5 residues within 4Å: Chain A: K.18, G.19, A.21, E.22, H.409 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:K.18, A:K.18 Hydrogen bonds: A:G.19, A:E.22, A:E.22 Salt bridges: A:H.409, A:H.409

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Benvenuti, M. et al., The two CO-dehydrogenases of Thermococcus sp. AM4. Biochim Biophys Acta Bioenerg (2020)

Release Date

2020-11-18

Peptides

Carbon monoxide dehydrogenase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
D

Carbon monoxide dehydrogenase

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