SMTL ID : 6ytt.1

CO-dehydrogenase/Acetyl-CoA synthase (CODH/ACS) from Clostridium autoethanogenum at 3.0-A resolution

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.01 Å

Oligo State

hetero-2-2-mer

Ligands

11 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 3 residues within 4Å: Chain A: D.79, N.83, L.221 No protein-ligand interaction detected (PLIP) GOL.2: 4 residues within 4Å: Chain A: T.271, Q.272, K.273 Chain B: I.424 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.271, A:Q.272, A:K.273 GOL.9: 2 residues within 4Å: Chain B: E.608, T.609 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.608, B:T.609 GOL.10: 6 residues within 4Å: Chain B: G.153, K.154, Q.155, L.156 Chain C: K.146, S.150 5 PLIP interactions: 1 interactions with chain C, 4 interactions with chain B Hydrogen bonds: C:K.146, B:G.153, B:Q.155, B:L.156, B:L.156 GOL.12: 4 residues within 4Å: Chain B: E.248, S.251, I.288, N.289 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.248, B:E.248, B:D.286 GOL.13: 3 residues within 4Å: Chain B: V.438, L.540, L.629 No protein-ligand interaction detected (PLIP) GOL.14: 5 residues within 4Å: Chain B: S.545, D.546, E.598, G.602, K.628 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:D.546, B:D.546, B:R.621, B:K.628 GOL.22: 3 residues within 4Å: Chain B: H.357, I.358 Chain C: D.201 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:D.201, B:I.358 GOL.23: 1 residues within 4Å: Chain C: L.629 No protein-ligand interaction detected (PLIP) GOL.24: 6 residues within 4Å: Chain B: K.146, S.150 Chain C: G.153, K.154, Q.155, L.156 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:Q.155, C:L.156, C:L.156, B:K.146 GOL.36: 3 residues within 4Å: Chain D: N.83, L.217, N.218 No protein-ligand interaction detected (PLIP)

2 x PE4: 2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL(Non-functional Binders)

PE4.3: 9 residues within 4Å: Chain A: G.253, T.267, L.268, E.284, A.285, R.286 Chain B: K.418, V.420, L.511 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.267, A:E.284, A:A.285, A:R.286 PE4.11: 5 residues within 4Å: Chain B: I.288, N.289, L.290, H.304, G.305 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:L.290

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

SF4.4: 12 residues within 4Å: Chain A: R.383, Y.387, C.485, L.487, C.488, H.495, C.497, L.506, C.507, C.574, C.576 Ligands: NI.8 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.485, A:C.488, A:C.497, A:C.507 SF4.15: 10 residues within 4Å: Chain B: C.38, G.41, C.46, R.48, R.56 Chain C: C.38, G.41, C.46, R.48, R.56 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain B, Metal complexes: C:C.38, C:C.46, B:C.38, B:C.46 SF4.16: 10 residues within 4Å: Chain B: C.47, N.49, C.50, M.52, G.53, C.55, G.68, C.70, R.80, I.196 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.47, B:C.50, B:C.55, B:C.70 SF4.25: 10 residues within 4Å: Chain C: C.47, N.49, C.50, M.52, C.55, I.69, C.70, I.77, R.80, I.196 4 PLIP interactions: 4 interactions with chain C, Metal complexes: C:C.47, C:C.50, C:C.55, C:C.70 SF4.37: 11 residues within 4Å: Chain D: R.383, C.485, L.487, C.488, C.497, L.506, C.507, V.510, C.574, C.576 Ligands: NI.38 3 PLIP interactions: 3 interactions with chain D, Metal complexes: D:C.485, D:C.488, D:C.507

9 x F: FLUORIDE ION(Non-covalent)

F.5: 1 residues within 4Å: Chain A: K.99 No protein-ligand interaction detected (PLIP) F.6: 1 residues within 4Å: Chain A: H.386 No protein-ligand interaction detected (PLIP) F.18: 3 residues within 4Å: Chain B: G.322, H.346, D.390 No protein-ligand interaction detected (PLIP) F.27: 2 residues within 4Å: Chain B: R.56 Chain C: R.56 No protein-ligand interaction detected (PLIP) F.28: 1 residues within 4Å: Chain C: K.207 No protein-ligand interaction detected (PLIP) F.29: 2 residues within 4Å: Chain C: E.598, K.628 No protein-ligand interaction detected (PLIP) F.30: 3 residues within 4Å: Chain B: K.355 Chain C: R.181, R.185 No protein-ligand interaction detected (PLIP) F.31: 2 residues within 4Å: Chain C: G.322, H.346 No protein-ligand interaction detected (PLIP) F.32: 2 residues within 4Å: Chain C: H.236, E.410 No protein-ligand interaction detected (PLIP)

4 x NI: NICKEL (II) ION(Non-covalent)

NI.7: 6 residues within 4Å: Chain A: L.506, C.574, G.575, C.576, F.577 Ligands: NI.8 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:C.574, A:C.576 NI.8: 5 residues within 4Å: Chain A: C.488, C.574, C.576 Ligands: SF4.4, NI.7 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:C.488, A:C.574, A:C.576 NI.38: 5 residues within 4Å: Chain D: C.488, C.574, C.576 Ligands: SF4.37, NI.39 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:C.488, D:C.574, D:C.576 NI.39: 6 residues within 4Å: Chain D: L.506, C.574, G.575, C.576, F.577 Ligands: NI.38 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:C.574

2 x XCC: FE(4)-NI(1)-S(4) CLUSTER(Non-covalent)

XCC.17: 10 residues within 4Å: Chain B: H.259, C.295, F.312, C.333, G.450, C.451, C.481, C.523, S.558, K.560 6 PLIP interactions: 6 interactions with chain B, Metal complexes: B:H.259, B:C.295, B:C.333, B:C.451, B:C.481, B:C.523 XCC.26: 8 residues within 4Å: Chain C: H.259, C.295, C.333, G.450, C.451, C.481, C.523, S.558 6 PLIP interactions: 6 interactions with chain C, Metal complexes: C:H.259, C:C.295, C:C.333, C:C.451, C:C.481, C:C.523

6 x NA: SODIUM ION(Non-functional Binders)

NA.19: 1 residues within 4Å: Chain B: E.226 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.226, B:E.226 NA.20: 3 residues within 4Å: Chain B: S.342, Y.345, T.347 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:T.347 NA.21: 2 residues within 4Å: Chain B: N.595, D.599 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.595, B:D.599 NA.33: 1 residues within 4Å: Chain C: E.608 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:E.608 NA.34: 1 residues within 4Å: Chain C: E.226 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:E.226 NA.35: 2 residues within 4Å: Chain C: N.595, D.599 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:N.595, C:D.599

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lemaire, O.N. et al., Gas channel rerouting in a primordial enzyme: Structural insights of the carbon-monoxide dehydrogenase/acetyl-CoA synthase complex from the acetogen Clostridium autoethanogenum. Biochim Biophys Acta Bioenerg (2020)

Release Date

2020-11-04

Peptides

CO dehydrogenase/acetyl-CoA synthase complex, beta subunit: AD
Carbon-monoxide dehydrogenase (Acceptor),Carbon-monoxide dehydrogenase (Acceptor): BC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

D
D

B
B

C
C

CO dehydrogenase/acetyl-CoA synthase complex, beta subunit

Carbon-monoxide dehydrogenase (Acceptor),Carbon-monoxide dehydrogenase (Acceptor)

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