SMTL ID : 3i01.2 (1 other biounit)

Native structure of bifunctional carbon monoxide dehydrogenase/acetyl-CoA synthase from Moorella thermoacetica, water-bound C-cluster.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.15 Å

Oligo State

hetero-2-2-mer

Ligands

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

SF4.1: 8 residues within 4Å: Chain A: C.59, G.62, C.67, R.69 Chain B: C.59, G.62, C.67, R.69 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B, Metal complexes: A:C.59, A:C.67, B:C.59, B:C.67 SF4.2: 10 residues within 4Å: Chain A: C.68, C.71, A.73, G.74, C.76, G.88, I.89, C.90, R.100, M.221 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.68, A:C.71, A:C.76, A:C.90 SF4.5: 13 residues within 4Å: Chain A: M.584 Chain B: C.68, F.70, C.71, A.73, G.74, C.76, G.88, I.89, C.90, I.97, R.100, M.221 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.68, B:C.71, B:C.76, B:C.90 SF4.8: 12 residues within 4Å: Chain C: I.146, C.506, V.507, L.508, C.509, H.516, C.518, G.526, L.527, C.528, V.531 Ligands: CU1.9 4 PLIP interactions: 4 interactions with chain C, Metal complexes: C:C.506, C:C.509, C:C.518, C:C.528 SF4.13: 12 residues within 4Å: Chain D: I.146, C.506, L.508, C.509, C.518, G.526, L.527, C.528, V.531, C.595, C.597 Ligands: CU1.14 4 PLIP interactions: 4 interactions with chain D, Metal complexes: D:C.506, D:C.509, D:C.518, D:C.528

2 x XCC: FE(4)-NI(1)-S(4) CLUSTER(Non-covalent)

XCC.3: 11 residues within 4Å: Chain A: H.283, C.316, C.317, F.334, C.355, G.469, C.470, C.500, C.550, S.585, K.587 8 PLIP interactions: 6 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.283, A:C.317, A:C.355, A:C.470, A:C.500, A:C.550, H2O.7, H2O.7 XCC.6: 11 residues within 4Å: Chain B: H.283, C.316, C.317, F.334, C.355, G.469, C.470, C.500, C.550, S.585, K.587 8 PLIP interactions: 6 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:H.283, B:C.317, B:C.355, B:C.470, B:C.500, B:C.550, H2O.13, H2O.13

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 7 residues within 4Å: Chain A: T.81, A.94, G.612, S.613, D.614, L.615 Chain C: H.27 4 PLIP interactions: 1 interactions with chain C, 3 interactions with chain A Hydrogen bonds: C:H.27, A:G.612, A:D.614, A:L.615 GOL.7: 6 residues within 4Å: Chain B: A.94, W.95, S.613, D.614, L.615 Chain D: H.27 4 PLIP interactions: 1 interactions with chain D, 3 interactions with chain B Hydrogen bonds: D:H.27, B:W.95, B:S.613, B:D.614

2 x CU1: COPPER (I) ION(Non-covalent)

CU1.9: 6 residues within 4Å: Chain C: C.509, C.595, C.597 Ligands: SF4.8, NI.10, ACT.11 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:C.509, C:C.595, C:C.597 CU1.14: 6 residues within 4Å: Chain D: C.509, C.595, C.597 Ligands: SF4.13, NI.15, ACT.16 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:C.509, D:C.595, D:C.597

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

NI.10: 7 residues within 4Å: Chain C: L.527, C.595, G.596, C.597, F.598 Ligands: CU1.9, ACT.11 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:C.595 NI.15: 7 residues within 4Å: Chain D: L.527, C.595, G.596, C.597, F.598 Ligands: CU1.14, ACT.16 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:C.595, D:C.597

2 x ACT: ACETATE ION(Non-functional Binders)

ACT.11: 7 residues within 4Å: Chain C: V.149, F.229, C.509, A.513, C.595 Ligands: CU1.9, NI.10 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:F.229, C:A.513 ACT.16: 10 residues within 4Å: Chain D: G.145, I.146, V.149, F.229, C.509, F.512, C.595, C.597 Ligands: CU1.14, NI.15 3 PLIP interactions: 3 interactions with chain D Hydrophobic interactions: D:V.149, D:F.229, D:F.512

2 x NA: SODIUM ION(Non-functional Binders)

NA.12: 6 residues within 4Å: Chain C: F.328, E.331, N.412, G.414, G.416, L.417 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:E.331, C:G.416, C:L.417 NA.17: 5 residues within 4Å: Chain D: F.328, E.331, N.412, G.414, L.417 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:E.331, D:N.412, D:L.417

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kung, Y. et al., Crystallographic snapshots of cyanide- and water-bound C-clusters from bifunctional carbon monoxide dehydrogenase/acetyl-CoA synthase. Biochemistry (2009)

Release Date

2009-09-01

Peptides

Carbon monoxide dehydrogenase/acetyl-CoA synthase subunit beta: AB
Carbon monoxide dehydrogenase/acetyl-CoA synthase subunit alpha: CD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

C
O

D
P

Carbon monoxide dehydrogenase/acetyl-CoA synthase subunit beta

Carbon monoxide dehydrogenase/acetyl-CoA synthase subunit alpha

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