SMTL ID : 7vw6.1

Cryo-EM Structure of Formate Dehydrogenase 1 from Methylorubrum extorquens AM1

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-mer

Ligands

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

SF4.1: 13 residues within 4Å: Chain A: C.213, I.214, Q.215, C.216, N.217, L.218, C.219, V.243, C.266, P.267, T.268, A.270, L.271 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.213, A:C.216, A:C.219, A:C.266 SF4.2: 12 residues within 4Å: Chain A: M.206, C.223, N.229, V.231, I.232, F.245, C.256, V.257, A.258, C.259, G.260, C.262 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.223, A:C.256, A:C.259, A:C.262 SF4.4: 12 residues within 4Å: Chain A: C.295, Y.297, C.298, V.300, G.301, C.302, L.328, C.329, K.331, G.332, P.478, V.479 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.295, A:C.298, A:C.302, A:C.329 SF4.10: 13 residues within 4Å: Chain B: I.330, P.348, S.501, C.502, G.503, Q.504, C.505, C.508, S.540, I.541, C.542, L.544, G.545 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.502, B:C.505, B:C.508, B:C.542

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

FES.3: 10 residues within 4Å: Chain A: H.100, L.101, C.102, H.103, G.113, N.114, C.115, R.116, C.118, C.132 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.102, A:C.115, A:C.118, A:C.132 FES.9: 9 residues within 4Å: Chain B: C.113, S.115, T.117, C.118, C.146, V.147, G.148, L.149, C.150 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.113, B:C.118, B:C.146, B:C.150

2 x MGD: 2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,7,8A,9-TETRAHYDRO-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-4-ONE GUANOSINE DINUCLEOTIDE(Non-covalent)

MGD.5: 33 residues within 4Å: Chain A: K.407, C.432, L.435, C.436, M.594, Q.598, Q.632, G.698, E.699, N.700, S.704, Q.724, D.725, L.726, A.741, S.742, A.743, F.744, K.747, D.774, T.873, R.875, W.880, H.881, T.882, M.885, F.947, N.955, F.971, K.972 Ligands: MGD.6, W.7, UNX.8 26 PLIP interactions: 26 interactions with chain A Hydrogen bonds: A:Q.598, A:Q.632, A:G.698, A:G.698, A:N.700, A:N.700, A:S.704, A:S.704, A:L.726, A:K.747, A:K.747, A:T.873, A:R.875, A:R.875, A:W.880, A:T.882, A:N.955, A:N.955, A:K.972 Salt bridges: A:D.774, A:H.881, A:H.881 pi-Stacking: A:F.947, A:F.971 pi-Cation interactions: A:F.947, A:F.971 MGD.6: 35 residues within 4Å: Chain A: K.331, C.436, I.469, G.470, A.471, N.472, V.475, N.476, H.477, D.499, P.500, R.501, Q.503, F.515, P.517, G.518, D.520, G.593, M.594, G.595, H.599, G.631, Q.632, S.872, G.874, R.875, V.876, L.877, H.879, W.880, H.881, K.972 Ligands: MGD.5, W.7, UNX.8 18 PLIP interactions: 18 interactions with chain A Hydrogen bonds: A:N.472, A:V.475, A:N.476, A:N.476, A:R.501, A:R.501, A:Q.503, A:G.518, A:M.594, A:S.872, A:R.875, A:R.875, A:H.881 Salt bridges: A:D.520, A:R.875, A:R.875, A:K.972 pi-Stacking: A:W.880

1 x W: TUNGSTEN ION(Non-covalent)

W.7: 5 residues within 4Å: Chain A: C.436, R.875 Ligands: MGD.5, MGD.6, UNX.8 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:C.436

1 x UNX: UNKNOWN ATOM OR ION(Non-functional Binders)

UNX.8: 6 residues within 4Å: Chain A: C.436, Q.632, V.635 Ligands: MGD.5, MGD.6, W.7 No protein-ligand interaction detected (PLIP)

1 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.11: 18 residues within 4Å: Chain B: G.226, L.227, G.228, K.237, N.253, D.255, E.256, G.257, Y.329, G.332, E.333, E.334, I.367, N.368, N.369, T.372, G.543, L.544 16 PLIP interactions: 16 interactions with chain B Hydrophobic interactions: B:Y.329, B:Y.329, B:E.333, B:L.544 Hydrogen bonds: B:L.227, B:G.228, B:N.253, B:G.257, B:G.332, B:E.334, B:I.367, B:N.368, B:N.369, B:N.369, B:T.372 Salt bridges: B:K.237

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yoshikawa, T. et al., Multiple electron transfer pathways of tungsten-containing formate dehydrogenase in direct electron transfer-type bioelectrocatalysis. Chem.Commun.(Camb.) (2022)

Release Date

2022-06-01

Peptides

Formate dehydrogenase: A
Tungsten-containing formate dehydrogenase beta subunit: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Formate dehydrogenase

Tungsten-containing formate dehydrogenase beta subunit

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