SMTL ID : 6b6v.1

Crystal structure of Desulfovibrio vulgaris carbon monoxide dehydrogenase, as-isolated (protein batch 1), canonical C-cluster

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-dimer

Ligands

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

SF4.1: 12 residues within 4Å: Chain A: C.59, N.61, C.62, M.64, G.65, C.67, G.80, V.81, C.82, I.89, R.92, M.211 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.59, A:C.62, A:C.67, A:C.82 SF4.8: 12 residues within 4Å: Chain B: C.59, N.61, C.62, M.64, G.65, C.67, G.80, V.81, C.82, I.89, R.92, M.211 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.59, B:C.62, B:C.67, B:C.82

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

XCC.2: 12 residues within 4Å: Chain A: H.274, C.309, C.310, H.327, C.348, G.455, C.456, C.486, C.527, Y.561, S.562, K.564 6 PLIP interactions: 6 interactions with chain A, Metal complexes: A:H.274, A:C.310, A:C.348, A:C.456, A:C.486, A:C.527 XCC.9: 12 residues within 4Å: Chain B: H.274, C.309, C.310, H.327, C.348, G.455, C.456, C.486, C.527, Y.561, S.562, K.564 6 PLIP interactions: 6 interactions with chain B, Metal complexes: B:H.274, B:C.310, B:C.348, B:C.456, B:C.486, B:C.527

7 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 7 residues within 4Å: Chain A: P.369, R.372 Chain B: G.192, R.208, S.219, V.222, R.226 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:S.219, A:R.372 Water bridges: B:R.226 GOL.4: 6 residues within 4Å: Chain A: G.192, R.208, S.219, V.222, R.226 Chain B: P.369 7 PLIP interactions: 1 interactions with chain B, 6 interactions with chain A Hydrogen bonds: B:P.369, A:R.208, A:R.208, A:S.219, A:R.226 Water bridges: A:S.219, A:S.219 GOL.5: 3 residues within 4Å: Chain A: V.132, R.136, A.152 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.136, A:R.136 GOL.6: 6 residues within 4Å: Chain A: A.86, D.87, G.589, S.590, E.591, N.592 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.87, A:G.589, A:E.591, A:N.592 Water bridges: A:A.86 GOL.10: 7 residues within 4Å: Chain A: C.50, F.52, R.68 Chain B: C.50, F.52, R.68 Ligands: FES.7 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:R.68, B:R.68, B:R.68 GOL.11: 8 residues within 4Å: Chain B: D.111, Y.346, T.367, S.368, P.369, V.381, H.382, P.383 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.111, B:T.367 GOL.12: 8 residues within 4Å: Chain B: S.549, P.578, Q.602, G.606, H.625, A.628, R.629, R.632 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:S.549, B:Q.602, B:Q.602, B:H.625, B:R.629, B:R.632, B:R.632

1 x FES: FE2/S2 (INORGANIC) CLUSTER(Non-covalent)

FES.7: 11 residues within 4Å: Chain A: C.50, F.52, C.53, T.58, R.68 Chain B: C.50, F.52, C.53, T.58, R.68 Ligands: GOL.10 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B, Metal complexes: A:C.50, A:C.53, B:C.50, B:C.53

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wittenborn, E.C. et al., Redox-dependent rearrangements of the NiFeS cluster of carbon monoxide dehydrogenase. Elife (2018)

Release Date

2018-10-03

Peptides

Carbon monoxide dehydrogenase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Carbon monoxide dehydrogenase

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