SMTL ID : 9c0t.1

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

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-2-2-mer

Ligands

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

SF4.1: 10 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 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.75, A:C.78, A:C.83, A:C.93 SF4.3: 5 residues within 4Å: Chain A: C.72, C.76 Chain B: C.72, Q.74, C.76 6 PLIP interactions: 3 interactions with chain B, 3 interactions with chain A, Salt bridges: B:E.104, A:E.104 Metal complexes: B:C.72, B:C.76, A:C.72, A:C.76 SF4.4: 9 residues within 4Å: Chain A: C.424, P.425, I.430, C.452, V.453, G.454, C.455, R.456, C.458 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.424, A:C.452, A:C.455, A:C.458 SF4.5: 12 residues within 4Å: Chain A: C.414, V.415, A.416, C.417, G.418, E.419, C.420, I.434, V.461, C.462, N.463, K.464 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.414, A:C.417, A:C.420, A:C.462 SF4.6: 10 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 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.75, B:C.78, B:C.83, B:C.93 SF4.8: 10 residues within 4Å: Chain B: A.423, C.424, P.425, I.430, C.452, V.453, 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 SF4.9: 12 residues within 4Å: Chain B: C.414, V.415, A.416, C.417, G.418, E.419, C.420, I.434, V.461, C.462, N.463, K.464 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.414, B:C.417, B:C.420, B:C.462 SF4.10: 12 residues within 4Å: Chain A: L.504 Chain E: C.189, L.191, C.192, N.199, C.201, S.209, L.210, C.211, I.214, C.280 Ligands: NI.11 4 PLIP interactions: 4 interactions with chain E, Metal complexes: E:C.189, E:C.192, E:C.201, E:C.211 SF4.14: 10 residues within 4Å: Chain F: C.189, L.191, C.192, C.201, S.209, L.210, C.211, I.214, C.280 Ligands: NI.15 4 PLIP interactions: 4 interactions with chain F, Metal complexes: F:C.189, F:C.192, F:C.201, F:C.211

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

RQM.2: 12 residues within 4Å: Chain A: H.249, C.276, C.277, I.301, C.322, G.519, C.520, C.549, C.584, Y.631, S.632, K.634 7 PLIP interactions: 7 interactions with chain A, Metal complexes: A:H.249, A:C.277, A:C.322, A:C.520, A:C.549, A:C.584, A:C.584 RQM.7: 12 residues within 4Å: Chain B: H.249, C.276, C.277, I.301, 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

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

NI.11: 6 residues within 4Å: Chain E: C.192, C.278, C.280 Ligands: SF4.10, NI.12, CMO.13 3 PLIP interactions: 3 interactions with chain E Metal complexes: E:C.192, E:C.278, E:C.280 NI.12: 6 residues within 4Å: Chain E: L.210, C.278, G.279, C.280 Ligands: NI.11, CMO.13 2 PLIP interactions: 2 interactions with chain E Metal complexes: E:C.278, E:C.280 NI.15: 6 residues within 4Å: Chain F: C.192, C.278, C.280 Ligands: SF4.14, NI.16, CMO.17 3 PLIP interactions: 3 interactions with chain F Metal complexes: F:C.192, F:C.278, F:C.280 NI.16: 5 residues within 4Å: Chain F: C.278, G.279, C.280 Ligands: NI.15, CMO.17 2 PLIP interactions: 2 interactions with chain F Metal complexes: F:C.278, F:C.280

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

CMO.13: 8 residues within 4Å: Chain A: G.503, V.507, F.601 Chain E: C.192, C.278, C.280 Ligands: NI.11, NI.12 No protein-ligand interaction detected (PLIP) CMO.17: 8 residues within 4Å: Chain B: G.503, V.507, F.601 Chain F: C.192, C.278, C.280 Ligands: NI.15, NI.16 No protein-ligand interaction detected (PLIP)

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: EF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

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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