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

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.43 Å

Oligo State

homo-dimer

Ligands

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

SF4.1: 12 residues within 4Å: Chain A: C.55, N.57, C.58, M.60, G.61, C.63, G.75, V.76, C.77, I.84, 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 SF4.9: 12 residues within 4Å: Chain B: C.55, N.57, C.58, M.60, G.61, C.63, G.75, V.76, C.77, I.84, 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: 7 residues within 4Å: Chain A: C.46, G.49, C.54, R.64 Chain B: C.46, R.56 Ligands: FES.10 2 PLIP interactions: 2 interactions with chain A, Metal complexes: A:C.46, A:C.54 FES.10: 7 residues within 4Å: Chain A: C.46, R.56 Chain B: C.46, G.49, C.54, 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.11: 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 5 PLIP interactions: 5 interactions with chain B, Metal complexes: B:H.269, B:C.305, B:C.343, B:C.451, B:C.481

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

PO4.4: 2 residues within 4Å: Chain A: E.22, H.409 3 PLIP interactions: 3 interactions with chain A Water bridges: A:E.22, A:H.409 Salt bridges: A:H.409 PO4.12: 2 residues within 4Å: Chain B: E.22, H.409 3 PLIP interactions: 3 interactions with chain B Water bridges: B:E.22, B:H.409 Salt bridges: B:H.409

6 x BU3: (R,R)-2,3-BUTANEDIOL(Non-covalent)

BU3.5: 9 residues within 4Å: Chain A: T.361, H.367, I.368, P.369, G.370, A.371, V.372, H.373 Chain B: D.211 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:H.367, A:H.373 Hydrogen bonds: A:T.361 BU3.6: 5 residues within 4Å: Chain A: R.438, L.539, V.541, L.628, W.630 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.539, A:V.541 Hydrogen bonds: A:R.438, A:L.628 BU3.7: 4 residues within 4Å: Chain A: K.258, E.259, D.260, Y.261 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:K.258 Hydrogen bonds: A:E.259, A:D.260 BU3.13: 9 residues within 4Å: Chain A: D.211 Chain B: T.361, H.367, I.368, P.369, G.370, A.371, V.372, H.373 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:H.367, B:H.373 Hydrogen bonds: B:T.361 BU3.14: 5 residues within 4Å: Chain B: R.438, L.539, V.541, L.628, W.630 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:L.539, B:V.541 Hydrogen bonds: B:R.438, B:L.628 BU3.15: 4 residues within 4Å: Chain B: K.258, E.259, D.260, Y.261 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:K.258 Hydrogen bonds: B:E.259, B:D.260

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

PEG.8: 4 residues within 4Å: Chain A: F.573, T.593, K.603, V.620 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.603 PEG.16: 4 residues within 4Å: Chain B: F.573, T.593, K.603, V.620 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.603

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
B

B
B

Carbon monoxide dehydrogenase

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