SMTL ID : 3cf4.2 (1 other biounit)

Structure of the CODH component of the M. barkeri ACDS complex

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

hetero-1-1-mer

Ligands

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

SF4.1: 3 residues within 4Å: Chain A: C.73, Q.75, C.77 2 PLIP interactions: 2 interactions with chain A, Metal complexes: A:C.73, A:C.77 SF4.2: 12 residues within 4Å: Chain A: C.76, Y.78, C.79, Y.81, G.82, C.84, G.92, A.93, C.94, I.96, R.104, A.184 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.76, A:C.79, A:C.84, A:C.94 SF4.6: 12 residues within 4Å: Chain A: C.427, P.428, I.431, I.433, C.455, I.456, G.457, C.458, R.459, R.460, C.461, I.475 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.427, A:C.455, A:C.458, A:C.461 SF4.7: 12 residues within 4Å: Chain A: C.417, A.418, D.419, C.420, G.421, A.422, C.423, P.434, M.437, C.465, K.467, I.471 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.417, A:C.420, A:C.423, A:C.465

1 x FE: FE (III) ION(Non-covalent)

FE.3: 5 residues within 4Å: Chain A: H.250, C.278, C.587, K.637 Ligands: WCC.4 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.250, A:C.278, A:C.587, H2O.1

1 x WCC: FE(3)-NI(1)-S(4) CLUSTER(Non-covalent)

WCC.4: 14 residues within 4Å: Chain A: H.250, C.277, C.278, C.323, G.522, C.523, P.524, C.552, C.587, F.634, S.635, K.637 Ligands: FE.3, CMO.5 6 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions, 1 Ligand-Ligand interactions Metal complexes: A:C.323, A:C.523, A:C.552, A:C.587, H2O.1, CMO.5

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

CMO.5: 5 residues within 4Å: Chain A: H.117, C.587, K.637, I.641 Ligands: WCC.4 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.117

11 x ACY: ACETIC ACID(Non-functional Binders)

ACY.8: 5 residues within 4Å: Chain A: D.327, P.330, E.331, K.334, R.459 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:P.330 Hydrogen bonds: A:D.327, A:E.331 Water bridges: A:K.334, A:R.459 Salt bridges: A:K.334, A:R.459 ACY.9: 3 residues within 4Å: Chain A: T.406, D.407, K.477 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.407 Salt bridges: A:K.477 ACY.10: 2 residues within 4Å: Chain A: R.571, F.572 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.572 Salt bridges: A:R.571 ACY.11: 6 residues within 4Å: Chain A: P.707, M.708, K.711, W.730, H.734 Chain B: Y.84 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Water bridges: A:K.711 Salt bridges: A:K.711, A:H.734 Hydrophobic interactions: B:Y.84 ACY.12: 5 residues within 4Å: Chain A: E.430, D.432 Chain B: K.117, R.141 Ligands: GOL.21 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:D.432 Water bridges: A:E.430, B:K.117 Salt bridges: B:K.117 ACY.13: 2 residues within 4Å: Chain A: P.351, R.353 2 PLIP interactions: 2 interactions with chain A Water bridges: A:R.353 Salt bridges: A:R.353 ACY.14: 6 residues within 4Å: Chain A: P.67, V.68, I.69, K.99 Chain B: A.127, F.131 6 PLIP interactions: 2 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:A.127, B:F.131 Hydrogen bonds: A:I.69 Water bridges: A:K.99, A:K.99 Salt bridges: A:K.99 ACY.15: 5 residues within 4Å: Chain A: M.731, E.732, K.735, E.742, T.760 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:M.731, A:E.732, A:K.735 Hydrogen bonds: A:E.742 Salt bridges: A:K.735 ACY.16: 4 residues within 4Å: Chain A: L.108, R.109, T.112, Q.636 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.108 Hydrogen bonds: A:Q.636 Salt bridges: A:R.109 ACY.17: 4 residues within 4Å: Chain A: R.607, R.623, Q.796 Ligands: GOL.18 2 PLIP interactions: 2 interactions with chain A Water bridges: A:R.607 Salt bridges: A:R.623 ACY.20: 4 residues within 4Å: Chain A: T.669, E.744 Chain B: Y.93, W.99 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:E.744 Hydrophobic interactions: B:Y.93

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.18: 7 residues within 4Å: Chain A: R.607, D.618, Y.619, R.623, Q.796, P.797 Ligands: ACY.17 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.607, A:R.607, A:R.623, A:R.623, A:Q.796 Water bridges: A:D.618 GOL.19: 10 residues within 4Å: Chain A: M.259, L.283, Y.286, K.287, E.288, R.292, P.293, P.294, Y.295, A.296 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:K.287, A:E.288, A:P.293, A:Y.295, A:A.296, A:A.296 GOL.21: 8 residues within 4Å: Chain A: L.424, L.425 Chain B: K.118, R.141, G.142, N.153, L.154 Ligands: ACY.12 6 PLIP interactions: 4 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:K.118, B:N.153 Water bridges: B:R.141, B:L.154, A:E.430, A:E.430

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

PEG.22: 7 residues within 4Å: Chain B: L.125, K.129, L.134, T.136, N.146, A.147, T.148 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:T.136

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gong, W. et al., Structure of the alpha2 epsilon2 Ni-dependent CO dehydrogenase component of the Methanosarcina barkeri acetyl-CoA decarboxylase/synthase complex. Proc.Natl.Acad.Sci.USA (2008)

Release Date

2008-07-22

Peptides

Acetyl-CoA decarboxylase/synthase alpha subunit: A
Acetyl-CoA decarboxylase/synthase epsilon subunit: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
G

Acetyl-CoA decarboxylase/synthase alpha subunit

Acetyl-CoA decarboxylase/synthase epsilon subunit

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