SMTL ID : 9c0s.1

Carbon monoxide dehydrogenase/acetyl-CoA synthase (CODH/ACS) pentamer from Methanosarcina thermophila

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-2-1-mer

Ligands

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

SF4.1: 11 residues within 4Å: Chain A: C.75, Y.77, C.78, F.80, G.81, C.83, G.91, A.92, C.93, R.103, A.183 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.75, A:C.78, A:C.83, A:C.93 SF4.3: 10 residues within 4Å: Chain A: C.424, P.425, I.430, C.452, V.453, G.454, C.455, R.456, R.457, C.458 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.424, A:C.452, A:C.455, A:C.458 SF4.4: 10 residues within 4Å: Chain A: C.414, V.415, A.416, C.417, G.418, E.419, C.420, C.462, N.463, I.468 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.414, A:C.417, A:C.420, A:C.462 SF4.7: 8 residues within 4Å: Chain A: C.72, Q.74, C.75, C.76, E.104 Chain B: C.72, C.76 Ligands: F3S.5 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A, Salt bridges: B:E.104, A:E.104 Metal complexes: B:C.72, B:C.76, A:C.72 SF4.8: 11 residues within 4Å: Chain B: C.75, Y.77, C.78, F.80, G.81, C.83, G.91, A.92, C.93, R.103, A.183 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.75, B:C.78, B:C.83, B:C.93 SF4.10: 10 residues within 4Å: Chain B: C.424, P.425, I.430, C.452, V.453, G.454, C.455, R.456, R.457, C.458 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.424, B:C.452, B:C.455, B:C.458 SF4.11: 10 residues within 4Å: Chain B: C.414, V.415, A.416, C.417, G.418, E.419, C.420, P.431, I.434, C.462 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.414, B:C.417, B:C.420, B:C.462 SF4.12: 11 residues within 4Å: Chain A: M.508 Chain E: C.189, L.191, C.192, C.201, S.209, L.210, C.211, I.214, C.280 Ligands: NI.13 4 PLIP interactions: 4 interactions with chain E, Metal complexes: E:C.189, E:C.192, E:C.201, E:C.211

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

RQM.2: 11 residues within 4Å: Chain A: H.249, C.276, C.277, C.322, G.519, C.520, C.549, C.584, Y.631, S.632, K.634 6 PLIP interactions: 6 interactions with chain A, Metal complexes: A:H.249, A:C.277, A:C.322, A:C.520, A:C.549, A:C.584 RQM.9: 11 residues within 4Å: Chain B: H.249, C.276, C.277, C.322, G.519, C.520, C.549, C.584, Y.631, S.632, K.634 6 PLIP interactions: 6 interactions with chain B, Metal complexes: B:H.249, B:C.277, B:C.322, B:C.520, B:C.549, B:C.584

1 x F3S: FE3-S4 CLUSTER(Non-covalent)

F3S.5: 7 residues within 4Å: Chain A: C.72, Q.74, C.75, C.76 Chain B: C.72, C.76 Ligands: SF4.7 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A, Metal complexes: B:C.72, B:C.76, A:C.72, A:C.76

1 x CMO: CARBON MONOXIDE(Non-functional Binders)

CMO.6: 8 residues within 4Å: Chain A: G.503, V.507, F.601 Chain E: C.192, C.278, C.280 Ligands: NI.13, NI.14 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.503

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

NI.13: 6 residues within 4Å: Chain E: C.192, C.278, C.280 Ligands: CMO.6, SF4.12, NI.14 3 PLIP interactions: 3 interactions with chain E Metal complexes: E:C.192, E:C.278, E:C.280 NI.14: 5 residues within 4Å: Chain E: C.278, G.279, C.280 Ligands: CMO.6, NI.13 2 PLIP interactions: 2 interactions with chain E Metal complexes: E:C.278, E:C.280

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Biester, A. et al., Capturing a methanogenic carbon monoxide dehydrogenase/acetyl-CoA synthase complex via cryogenic electron microscopy. Proc.Natl.Acad.Sci.USA (2024)

Release Date

2024-10-16

Peptides

Acetyl-CoA decarbonylase/synthase complex subunit alpha 2: AB
Acetyl-CoA decarbonylase/synthase complex subunit epsilon 2: CD
Acetyl-CoA decarbonylase/synthase complex subunit beta 2: E

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

Acetyl-CoA decarbonylase/synthase complex subunit alpha 2

Acetyl-CoA decarbonylase/synthase complex subunit epsilon 2

Acetyl-CoA decarbonylase/synthase complex subunit beta 2

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