SMTL ID : 9fzz.1

Structure of carbon monoxide dehydrogenase/acetyl-CoA synthase (CODH/ACS) in complex with corrinoid iron-sulfur protein (CoFeSP) from Clostridium autoethanogenum (composite structure, class 3B)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 2.65 Å

Oligo State

hetero-2-1-2-1-mer

Ligands

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

SF4.1: 11 residues within 4Å: Chain A: C.485, L.487, C.488, H.495, C.497, L.506, C.507, V.510, C.574, C.576 Ligands: NI.2 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.485, A:C.488, A:C.497, A:C.507 SF4.4: 10 residues within 4Å: Chain D: C.37, G.40, C.45, R.47, R.55 Chain E: C.37, G.40, C.45, R.47, R.55 4 PLIP interactions: 2 interactions with chain E, 2 interactions with chain D, Metal complexes: E:C.37, E:C.45, D:C.37, D:C.45 SF4.5: 11 residues within 4Å: Chain D: C.46, N.48, C.49, M.51, G.52, C.54, G.67, I.68, C.69, R.79, I.195 4 PLIP interactions: 4 interactions with chain D, Metal complexes: D:C.46, D:C.49, D:C.54, D:C.69 SF4.7: 11 residues within 4Å: Chain E: C.46, N.48, C.49, M.51, G.52, C.54, G.67, I.68, C.69, R.79, I.195 4 PLIP interactions: 4 interactions with chain E, Metal complexes: E:C.46, E:C.49, E:C.54, E:C.69 SF4.9: 10 residues within 4Å: Chain F: P.13, N.16, C.17, K.18, C.20, C.25, F.28, C.42, P.43, H.44 4 PLIP interactions: 4 interactions with chain F, Metal complexes: F:C.17, F:C.20, F:C.25, F:C.42

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

NI.2: 6 residues within 4Å: Chain A: C.488, L.506, C.574, C.576 Ligands: SF4.1, NI.3 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:C.488, A:C.574, A:C.576 NI.3: 7 residues within 4Å: Chain A: F.491, L.506, C.574, G.575, C.576, F.577 Ligands: NI.2 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:C.574, A:C.576

2 x RQM: Fe(3)-Ni(1)-S(4) cluster(Non-covalent)

RQM.6: 12 residues within 4Å: Chain D: H.258, C.293, C.294, F.311, C.332, G.449, C.450, C.480, C.522, M.556, S.557, K.559 6 PLIP interactions: 6 interactions with chain D, Metal complexes: D:H.258, D:C.294, D:C.332, D:C.450, D:C.480, D:C.522 RQM.8: 12 residues within 4Å: Chain E: H.258, C.293, C.294, F.311, C.332, G.449, C.450, C.480, C.522, M.556, S.557, K.559 6 PLIP interactions: 6 interactions with chain E, Metal complexes: E:H.258, E:C.294, E:C.332, E:C.450, E:C.480, E:C.522

1 x B12: COBALAMIN(Non-covalent)

B12.10: 27 residues within 4Å: Chain A: L.487, S.490, F.491 Chain B: Y.220 Chain F: P.321, L.341, C.342, T.343, F.346, L.348, T.349, L.352, G.373, Y.374, S.375, V.376, L.377, T.378, A.381, A.382, P.411, K.413, S.433, S.434, T.435, A.437, I.440 18 PLIP interactions: 15 interactions with chain F, 3 interactions with chain A, Hydrophobic interactions: F:L.341, F:L.341, F:L.348, F:L.377, F:A.381, F:P.411, F:I.440, A:F.491 Hydrogen bonds: F:T.343, F:T.349, F:G.373, F:Y.374, F:S.375, F:V.376, F:A.437, A:S.490, A:S.490 Metal complexes: F:T.378

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

2025-02-05

Peptides

CO-methylating acetyl-CoA synthase: AC
Acetyl-CoA decarbonylase/synthase complex subunit delta: B
Carbon monoxide dehydrogenase/acetyl-CoA synthase beta subunit: DE
Corrinoid iron-sulfur protein large subunit: F

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

C
A

B
E

D
B

E
C

F
F

CO-methylating acetyl-CoA synthase

Acetyl-CoA decarbonylase/synthase complex subunit delta

Carbon monoxide dehydrogenase/acetyl-CoA synthase beta subunit

Corrinoid iron-sulfur protein large subunit

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