SMTL ID : 8x9g.1

Crystal structure of CO dehydrogenase mutant in complex with BV

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.11 Å

Oligo State

homo-dimer

Ligands

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

SF4.1: 12 residues within 4Å: Chain A: C.68, R.69, H.70, C.71, Q.73, G.74, C.76, I.89, C.90, A.92, R.100, M.219 3 PLIP interactions: 3 interactions with chain A, Metal complexes: A:C.68, A:C.76, A:C.90 SF4.6: 12 residues within 4Å: Chain B: C.68, R.69, H.70, C.71, Q.73, G.74, C.76, I.89, C.90, A.92, R.100, M.219 3 PLIP interactions: 3 interactions with chain B, Metal complexes: B:C.68, B:C.76, B:C.90

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

FES.2: 7 residues within 4Å: Chain A: C.59, F.61, G.62, C.67 Chain B: C.67, R.69 Ligands: FES.7 2 PLIP interactions: 2 interactions with chain A, Metal complexes: A:C.59, A:C.67 FES.7: 7 residues within 4Å: Chain A: C.67, R.69 Chain B: C.59, F.61, G.62, C.67 Ligands: FES.2 2 PLIP interactions: 2 interactions with chain B, Metal complexes: B:C.59, B:C.67

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

XCC.3: 12 residues within 4Å: Chain A: H.281, C.314, C.315, S.332, C.353, G.465, C.466, C.496, C.546, M.580, H.581, K.583 7 PLIP interactions: 7 interactions with chain A, Metal complexes: A:H.281, A:C.315, A:C.353, A:C.466, A:C.496, A:C.546, A:C.546 XCC.8: 12 residues within 4Å: Chain B: H.281, C.314, C.315, S.332, C.353, G.465, C.466, C.496, C.546, M.580, H.581, K.583 7 PLIP interactions: 7 interactions with chain B, Metal complexes: B:H.281, B:C.315, B:C.353, B:C.466, B:C.496, B:C.546, B:C.546

2 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.4: 5 residues within 4Å: Chain A: P.57, Q.58, C.59, G.60 Ligands: PGE.9 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.60 PGE.9: 5 residues within 4Å: Chain B: P.57, Q.58, C.59, G.60 Ligands: PGE.4 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:G.60

2 x S7L: 1-(phenylmethyl)-4-[1-(phenylmethyl)pyridin-1-ium-4-yl]pyridin-1-ium

S7L.5: 8 residues within 4Å: Chain A: E.63, T.64, P.80, F.81, L.603, T.607, G.608, L.632 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:P.80, A:F.81, A:L.603 S7L.10: 8 residues within 4Å: Chain B: E.63, T.64, P.80, F.81, L.603, T.607, G.608, L.632 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:P.80, B:F.81, B:L.603

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kim, S.M. et al., Identifying a key spot for electron mediator-interaction to tailor CO dehydrogenase's affinity. Nat Commun (2024)

Release Date

2024-04-17

Peptides

Carbon monoxide dehydrogenase 2: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Carbon monoxide dehydrogenase 2

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