SMTL ID : 3cf4.1 (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-2-2-mer

Ligands

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

SF4.1: 6 residues within 4Å: Chain A: C.73, Q.75, C.77 Chain C: C.73, C.77 Ligands: SF4.23 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 SF4.23: 6 residues within 4Å: Chain A: C.73, C.77 Chain C: C.73, Q.75, C.77 Ligands: SF4.1 2 PLIP interactions: 2 interactions with chain C, Metal complexes: C:C.73, C:C.77 SF4.24: 12 residues within 4Å: Chain C: 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 C, Metal complexes: C:C.76, C:C.79, C:C.84, C:C.94 SF4.28: 12 residues within 4Å: Chain C: 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 C, Metal complexes: C:C.427, C:C.455, C:C.458, C:C.461 SF4.29: 12 residues within 4Å: Chain C: 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 C, Metal complexes: C:C.417, C:C.420, C:C.423, C:C.465

2 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 FE.25: 5 residues within 4Å: Chain C: H.250, C.278, C.587, K.637 Ligands: WCC.26 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:H.250, C:C.278, C:C.587, H2O.21

2 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 WCC.26: 14 residues within 4Å: Chain C: 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.25, CMO.27 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions, Metal complexes: C:C.323, C:C.523, C:C.552, C:C.587, H2O.21

2 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 CMO.27: 5 residues within 4Å: Chain C: H.117, C.587, K.637, I.641 Ligands: WCC.26 No protein-ligand interaction detected (PLIP)

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

ACY.8: 6 residues within 4Å: Chain A: D.327, P.330, E.331, K.334, R.459 Chain C: R.91 Ligand excluded by PLIP ACY.9: 3 residues within 4Å: Chain A: T.406, D.407, K.477 Ligand excluded by PLIP ACY.10: 2 residues within 4Å: Chain A: R.571, F.572 Ligand excluded by PLIP ACY.11: 6 residues within 4Å: Chain A: P.707, M.708, K.711, W.730, H.734 Chain B: Y.84 Ligand excluded by PLIP ACY.12: 5 residues within 4Å: Chain A: E.430, D.432 Chain B: K.117, R.141 Ligands: GOL.21 Ligand excluded by PLIP ACY.13: 2 residues within 4Å: Chain A: P.351, R.353 Ligand excluded by PLIP ACY.14: 6 residues within 4Å: Chain A: P.67, V.68, I.69, K.99 Chain B: A.127, F.131 Ligand excluded by PLIP ACY.15: 5 residues within 4Å: Chain A: M.731, E.732, K.735, E.742, T.760 Ligand excluded by PLIP ACY.16: 6 residues within 4Å: Chain A: L.108, R.109, T.112, Q.636 Chain C: Y.78, V.182 Ligand excluded by PLIP ACY.17: 4 residues within 4Å: Chain A: R.607, R.623, Q.796 Ligands: GOL.18 Ligand excluded by PLIP ACY.20: 4 residues within 4Å: Chain A: T.669, E.744 Chain B: Y.93, W.99 Ligand excluded by PLIP ACY.30: 6 residues within 4Å: Chain A: R.91 Chain C: D.327, P.330, E.331, K.334, R.459 Ligand excluded by PLIP ACY.31: 3 residues within 4Å: Chain C: T.406, D.407, K.477 Ligand excluded by PLIP ACY.32: 2 residues within 4Å: Chain C: R.571, F.572 Ligand excluded by PLIP ACY.33: 6 residues within 4Å: Chain C: P.707, M.708, K.711, W.730, H.734 Chain D: Y.84 Ligand excluded by PLIP ACY.34: 5 residues within 4Å: Chain C: E.430, D.432 Chain D: K.117, R.141 Ligands: GOL.43 Ligand excluded by PLIP ACY.35: 2 residues within 4Å: Chain C: P.351, R.353 Ligand excluded by PLIP ACY.36: 6 residues within 4Å: Chain C: P.67, V.68, I.69, K.99 Chain D: A.127, F.131 Ligand excluded by PLIP ACY.37: 5 residues within 4Å: Chain C: M.731, E.732, K.735, E.742, T.760 Ligand excluded by PLIP ACY.38: 6 residues within 4Å: Chain A: Y.78, V.182 Chain C: L.108, R.109, T.112, Q.636 Ligand excluded by PLIP ACY.39: 4 residues within 4Å: Chain C: R.607, R.623, Q.796 Ligands: GOL.40 Ligand excluded by PLIP ACY.42: 4 residues within 4Å: Chain C: T.669, E.744 Chain D: Y.93, W.99 Ligand excluded by PLIP

6 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: 2 interactions with chain A, 4 interactions with chain B Water bridges: A:E.430, A:E.430, B:R.141, B:L.154 Hydrogen bonds: B:K.118, B:N.153 GOL.40: 7 residues within 4Å: Chain C: R.607, D.618, Y.619, R.623, Q.796, P.797 Ligands: ACY.39 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:R.607, C:R.607, C:R.623, C:R.623, C:Q.796 Water bridges: C:D.618 GOL.41: 10 residues within 4Å: Chain C: 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 C Hydrogen bonds: C:K.287, C:E.288, C:P.293, C:Y.295, C:A.296, C:A.296 GOL.43: 8 residues within 4Å: Chain C: L.424, L.425 Chain D: K.118, R.141, G.142, N.153, L.154 Ligands: ACY.34 6 PLIP interactions: 4 interactions with chain D, 2 interactions with chain C Hydrogen bonds: D:K.118, D:N.153 Water bridges: D:R.141, D:L.154, C:E.430, C:E.430

2 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 PEG.44: 7 residues within 4Å: Chain D: L.125, K.129, L.134, T.136, N.146, A.147, T.148 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D: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: AC
Acetyl-CoA decarboxylase/synthase epsilon subunit: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
A

B
G

D
G

Acetyl-CoA decarboxylase/synthase alpha subunit

Acetyl-CoA decarboxylase/synthase epsilon subunit

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