SMTL ID : 9g7i.1

Structure of carbon monoxide dehydrogenase/acetyl-CoA synthase (CODH/ACS) in complex with acetyl-Coenyzme A from Clostridium autoethanogenum

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.93 Å

Oligo State

hetero-2-2-mer

Ligands

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

SF4.1: 13 residues within 4Å: Chain A: R.383, Y.387, C.485, C.488, H.495, C.497, G.505, L.506, C.507, V.510, C.574, C.576 Ligands: NI.3 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.485, A:C.488, A:C.497, A:C.507 SF4.22: 11 residues within 4Å: Chain B: C.47, N.49, C.50, M.52, G.53, C.55, G.68, I.69, 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 SF4.49: 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 B, 2 interactions with chain C, Metal complexes: B:C.38, B:C.46, C:C.38, C:C.46 SF4.50: 10 residues within 4Å: Chain C: C.47, N.49, C.50, M.52, C.55, G.68, I.69, C.70, R.80, I.196 3 PLIP interactions: 3 interactions with chain C, Metal complexes: C:C.47, C:C.50, C:C.55 SF4.63: 13 residues within 4Å: Chain D: R.383, C.485, L.487, C.488, H.495, C.497, G.505, L.506, C.507, V.510, C.574, C.576 Ligands: NI.64 4 PLIP interactions: 4 interactions with chain D, Metal complexes: D:C.485, D:C.488, D:C.497, D:C.507

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

NI.2: 5 residues within 4Å: Chain A: C.574, G.575, C.576, F.577 Ligands: NI.3 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:C.574, A:C.576 NI.3: 5 residues within 4Å: Chain A: C.488, C.574, C.576 Ligands: SF4.1, NI.2 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:C.488, A:C.574, A:C.576 NI.64: 5 residues within 4Å: Chain D: C.488, C.574, C.576 Ligands: SF4.63, NI.65 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:C.488, D:C.574, D:C.576 NI.65: 5 residues within 4Å: Chain D: C.574, G.575, C.576, F.577 Ligands: NI.64 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:C.574, D:C.576

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

EDO.4: 6 residues within 4Å: Chain A: T.271, Q.272, K.273, K.277 Chain B: Q.423, I.424 Ligand excluded by PLIP EDO.6: 3 residues within 4Å: Chain A: M.1, T.6, E.240 Ligand excluded by PLIP EDO.15: 2 residues within 4Å: Chain A: G.211, K.213 Ligand excluded by PLIP EDO.16: 2 residues within 4Å: Chain A: T.129, D.131 Ligand excluded by PLIP EDO.17: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP EDO.18: 2 residues within 4Å: Chain A: I.67, S.70 Ligand excluded by PLIP EDO.19: 3 residues within 4Å: Chain A: T.9, K.12, Q.13 Ligand excluded by PLIP EDO.20: 4 residues within 4Å: Chain A: D.191, V.192, T.193, L.241 Ligand excluded by PLIP EDO.34: 1 residues within 4Å: Chain B: M.427 Ligand excluded by PLIP EDO.35: 4 residues within 4Å: Chain B: D.117, N.119, T.234, E.410 Ligand excluded by PLIP EDO.36: 4 residues within 4Å: Chain B: S.237, I.238, D.239, I.404 Ligand excluded by PLIP EDO.37: 3 residues within 4Å: Chain B: N.595, E.598, D.599 Ligand excluded by PLIP EDO.38: 4 residues within 4Å: Chain B: K.343, S.344, Y.345 Ligands: EDO.39 Ligand excluded by PLIP EDO.39: 4 residues within 4Å: Chain B: D.22, S.344, Y.345 Ligands: EDO.38 Ligand excluded by PLIP EDO.40: 4 residues within 4Å: Chain B: M.364, E.365, S.374, K.377 Ligand excluded by PLIP EDO.41: 4 residues within 4Å: Chain B: S.545, D.546, G.602, K.628 Ligand excluded by PLIP EDO.42: 7 residues within 4Å: Chain B: K.120, F.222, S.408, V.409, E.410, R.528, D.531 Ligand excluded by PLIP EDO.43: 3 residues within 4Å: Chain B: P.163, E.167, K.170 Ligand excluded by PLIP EDO.44: 4 residues within 4Å: Chain B: G.111, D.112, I.113, E.369 Ligand excluded by PLIP EDO.45: 2 residues within 4Å: Chain B: K.116, E.118 Ligand excluded by PLIP EDO.46: 2 residues within 4Å: Chain B: Q.155, L.156 Ligand excluded by PLIP EDO.47: 3 residues within 4Å: Chain B: F.232, G.233, R.303 Ligand excluded by PLIP EDO.48: 7 residues within 4Å: Chain B: S.127, F.128, T.160, P.162, W.218, M.223, E.226 Ligand excluded by PLIP EDO.51: 4 residues within 4Å: Chain C: E.598, R.621, E.624, K.628 Ligand excluded by PLIP EDO.57: 4 residues within 4Å: Chain C: F.232, H.236, R.303, H.304 Ligand excluded by PLIP EDO.58: 1 residues within 4Å: Chain C: N.620 Ligand excluded by PLIP EDO.59: 3 residues within 4Å: Chain C: N.595, E.598, D.599 Ligand excluded by PLIP EDO.60: 5 residues within 4Å: Chain C: E.123, V.124, S.127, P.163, E.226 Ligand excluded by PLIP EDO.61: 3 residues within 4Å: Chain C: G.62, K.63, G.64 Ligand excluded by PLIP EDO.62: 6 residues within 4Å: Chain B: K.146, L.149, S.150 Chain C: K.154, Q.155, L.156 Ligand excluded by PLIP EDO.72: 4 residues within 4Å: Chain D: L.471, L.474, P.501, E.502 Ligand excluded by PLIP EDO.73: 4 residues within 4Å: Chain D: N.670, P.700, K.703, M.704 Ligand excluded by PLIP EDO.74: 3 residues within 4Å: Chain D: E.141, C.142, P.143 Ligand excluded by PLIP EDO.75: 3 residues within 4Å: Chain C: K.418 Chain D: T.267, E.284 Ligand excluded by PLIP

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

PE4.5: 2 residues within 4Å: Chain A: E.141, K.167 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.141, A:K.167

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 2 residues within 4Å: Chain A: E.681, T.682 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.681 GOL.21: 4 residues within 4Å: Chain B: E.248, S.251, D.286, N.289 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.248, B:S.251, B:S.251 GOL.24: 3 residues within 4Å: Chain B: E.25, D.29, D.33 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.25, B:D.33 GOL.26: 3 residues within 4Å: Chain B: N.538, L.540, G.541 No protein-ligand interaction detected (PLIP) GOL.27: 3 residues within 4Å: Chain B: E.608, T.609, K.613 No protein-ligand interaction detected (PLIP) GOL.68: 3 residues within 4Å: Chain D: D.182, R.184, E.306 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:D.182

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

PEG.8: 5 residues within 4Å: Chain A: D.79, N.83, L.217, N.218, L.221 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.79 PEG.23: 3 residues within 4Å: Chain B: G.541, V.542, L.629 No protein-ligand interaction detected (PLIP) PEG.66: 2 residues within 4Å: Chain D: N.83, N.218 No protein-ligand interaction detected (PLIP)

10 x CA: CALCIUM ION(Non-covalent)

CA.9: 1 residues within 4Å: Chain A: D.39 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.39, H2O.1 CA.10: 1 residues within 4Å: Chain A: E.174 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:E.174 CA.11: 1 residues within 4Å: Chain A: E.141 No protein-ligand interaction detected (PLIP) CA.12: 1 residues within 4Å: Chain A: E.75 No protein-ligand interaction detected (PLIP) CA.28: 1 residues within 4Å: Chain B: E.226 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:E.226 CA.53: 2 residues within 4Å: Chain C: E.365, S.374 No protein-ligand interaction detected (PLIP) CA.54: 1 residues within 4Å: Chain C: D.239 No protein-ligand interaction detected (PLIP) CA.55: 2 residues within 4Å: Chain C: F.128, E.226 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:E.226 CA.70: 3 residues within 4Å: Chain D: R.645, D.705, P.706 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:D.705 CA.71: 3 residues within 4Å: Chain D: D.182, S.490, F.491 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:S.490

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

CL.13: 4 residues within 4Å: Chain A: G.253, P.255, A.285, R.286 Ligand excluded by PLIP CL.14: 1 residues within 4Å: Chain A: R.184 Ligand excluded by PLIP CL.29: 3 residues within 4Å: Chain B: T.429, V.430, R.535 Ligand excluded by PLIP CL.30: 3 residues within 4Å: Chain B: G.322, H.346, D.390 Ligand excluded by PLIP CL.31: 3 residues within 4Å: Chain B: V.24, E.25, K.340 Ligand excluded by PLIP CL.32: 2 residues within 4Å: Chain B: K.467, Y.489 Ligand excluded by PLIP CL.33: 1 residues within 4Å: Chain B: K.6 Ligand excluded by PLIP CL.56: 2 residues within 4Å: Chain C: T.429, V.430 Ligand excluded by PLIP

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

XCC.25: 10 residues within 4Å: Chain B: H.259, C.294, C.295, 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.52: 10 residues within 4Å: Chain C: H.259, C.295, C.333, G.450, C.451, G.480, C.481, C.523, S.558, K.560 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

1 x ACO: ACETYL COENZYME *A(Non-covalent)

ACO.67: 15 residues within 4Å: Chain D: R.309, I.310, R.311, K.312, G.321, H.386, V.398, G.399, W.405, R.407, C.488, F.491, G.575, C.576, R.595 8 PLIP interactions: 8 interactions with chain D Hydrogen bonds: D:R.311, D:G.399, D:R.595 Salt bridges: D:R.311, D:R.311, D:K.312, D:R.407 pi-Stacking: D:W.405

1 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.69: 4 residues within 4Å: Chain D: A.611, S.612, G.615, V.618 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:A.611

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yin, M.D. et al., Conformational dynamics of a multienzyme complex in anaerobic carbon fixation. Science (2025)

Release Date

2025-02-12

Peptides

CO-methylating acetyl-CoA synthase: AD
Carbon monoxide dehydrogenase: BC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

D
D

B
B

C
C

CO-methylating acetyl-CoA synthase

Carbon monoxide dehydrogenase

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