SMTL ID : 3i04.1 (1 other biounit)

Cyanide-bound structure of bifunctional carbon monoxide dehydrogenase/acetyl-CoA synthase from Moorella thermoacetica, cyanide-bound C-cluster

Coordinates

PDB Format

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.58, G.61, C.66, R.68 Chain B: C.58, G.61, C.66, R.68 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B, Metal complexes: A:C.58, A:C.66, B:C.58, B:C.66 SF4.2: 12 residues within 4Å: Chain A: C.67, F.69, C.70, A.72, G.73, C.75, G.87, C.89, I.96, R.99, M.220 Chain B: M.583 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.67, A:C.70, A:C.75, A:C.89 SF4.6: 11 residues within 4Å: Chain A: M.583 Chain B: C.67, F.69, C.70, A.72, G.73, C.75, G.87, C.89, R.99, M.220 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.67, B:C.70, B:C.75, B:C.89 SF4.11: 13 residues within 4Å: Chain C: I.145, C.505, L.507, C.508, H.515, C.517, G.525, L.526, C.527, V.530, C.594, C.596 Ligands: CU1.10 4 PLIP interactions: 4 interactions with chain C, Metal complexes: C:C.505, C:C.508, C:C.517, C:C.527 SF4.16: 12 residues within 4Å: Chain D: I.145, C.505, L.507, C.508, C.517, G.525, L.526, C.527, V.530, C.594, C.596 Ligands: CU1.15 4 PLIP interactions: 4 interactions with chain D, Metal complexes: D:C.505, D:C.508, D:C.517, D:C.527

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

XCC.3: 12 residues within 4Å: Chain A: H.282, C.315, C.316, F.333, C.354, G.468, C.469, C.499, C.549, S.584, K.586 Ligands: CYN.4 7 PLIP interactions: 6 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.282, A:C.316, A:C.354, A:C.469, A:C.499, A:C.549, H2O.12 XCC.7: 12 residues within 4Å: Chain B: H.282, C.315, C.316, F.333, C.354, G.468, C.469, C.499, C.549, S.584, K.586 Ligands: CYN.8 7 PLIP interactions: 6 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.282, B:C.316, B:C.354, B:C.469, B:C.499, B:C.549, H2O.27

2 x CYN: CYANIDE ION(Non-covalent)

CYN.4: 5 residues within 4Å: Chain A: H.112, C.549, K.586, I.590 Ligands: XCC.3 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.112 Water bridges: A:V.550 CYN.8: 7 residues within 4Å: Chain B: H.112, C.549, S.584, K.586, A.587, I.590 Ligands: XCC.7 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:H.112 Water bridges: B:V.550

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 5 residues within 4Å: Chain A: W.94, S.612, D.613, L.614 Chain C: H.26 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.613, A:L.614 GOL.9: 7 residues within 4Å: Chain B: T.80, W.94, S.612, D.613, L.614 Chain D: R.22, H.26 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.613, B:D.613, B:L.614

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

CU1.10: 7 residues within 4Å: Chain C: I.145, C.508, C.594, C.596 Ligands: SF4.11, NI.12, ACT.13 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:C.508, C:C.594, C:C.596 CU1.15: 7 residues within 4Å: Chain D: I.145, C.508, C.594, C.596 Ligands: SF4.16, ACT.18, NI.19 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:C.508, D:C.594, D:C.596

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

NI.12: 7 residues within 4Å: Chain C: L.526, C.594, G.595, C.596, F.597 Ligands: CU1.10, ACT.13 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:C.594, C:C.596 NI.19: 7 residues within 4Å: Chain D: L.526, C.594, G.595, C.596, F.597 Ligands: CU1.15, ACT.18 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:C.594, D:C.596

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

ACT.13: 10 residues within 4Å: Chain C: G.144, I.145, V.148, F.228, C.508, F.511, C.594, C.596 Ligands: CU1.10, NI.12 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:V.148, C:F.228, C:F.511 ACT.18: 9 residues within 4Å: Chain D: G.144, I.145, V.148, F.228, C.508, C.594, C.596 Ligands: CU1.15, NI.19 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:V.148, D:F.228

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

NA.14: 5 residues within 4Å: Chain C: F.327, E.330, N.411, G.413, L.416 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:E.330, C:L.416, C:L.416 NA.17: 5 residues within 4Å: Chain D: F.327, E.330, N.411, G.413, L.416 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:G.413, D:L.416

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
A

B
B

C
M

D
N

Carbon monoxide dehydrogenase/acetyl-CoA synthase subunit beta

Carbon monoxide dehydrogenase/acetyl-CoA synthase subunit alpha

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