SMTL ID : 6vw7.2 (1 other biounit)

Formate Dehydrogenase FdsABG subcomplex FdsBG from C. necator - NADH bound

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

hetero-1-1-mer

Ligands

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

FES.1: 10 residues within 4Å: Chain A: C.87, A.89, A.91, C.92, C.128, L.129, G.130, Q.131, C.132 Chain B: S.188 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.87, A:C.92, A:C.128, A:C.132

1 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.2: 20 residues within 4Å: Chain B: G.154, R.155, G.156, K.165, N.182, D.184, E.185, G.186, Y.270, G.273, E.274, E.275, I.308, N.309, N.310, S.313, C.489, A.490, M.491 Ligands: NAI.4 25 PLIP interactions: 25 interactions with chain B Hydrophobic interactions: B:Y.270, B:E.274, B:E.274, B:A.490, B:M.491 Hydrogen bonds: B:R.155, B:G.156, B:G.157, B:N.182, B:E.185, B:G.186, B:G.273, B:E.275, B:N.309, B:N.310, B:N.310, B:S.313 Water bridges: B:G.154, B:G.154, B:G.156, B:N.182, B:D.187, B:D.193, B:G.273 Salt bridges: B:K.165

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

SF4.3: 13 residues within 4Å: Chain B: V.271, V.289, S.442, C.443, G.444, K.445, C.446, C.449, S.487, L.488, C.489, M.491, G.492 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.443, B:C.446, B:C.449, B:C.489

1 x NAI: 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE(Non-covalent)

NAI.4: 10 residues within 4Å: Chain B: A.158, F.160, K.165, T.168, E.275, K.292, L.295, P.296, A.297 Ligands: FMN.2 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:K.165, B:E.275, B:K.292 Water bridges: B:A.158 Salt bridges: B:K.292, B:K.292 pi-Stacking: B:F.160

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Young, T. et al., Crystallographic and kinetic analyses of the FdsBG subcomplex of the cytosolic formate dehydrogenase FdsABG fromCupriavidus necator. J.Biol.Chem. (2020)

Release Date

2020-04-08

Peptides

NAD-dependent formate dehydrogenase gamma subunit: A
NAD-dependent formate dehydrogenase beta subunit: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

NAD-dependent formate dehydrogenase gamma subunit

NAD-dependent formate dehydrogenase beta subunit

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