SMTL ID : 8j83.1

Crystal structure of formate dehydrogenase from Methylorubrum extorquens AM1

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

hetero-1-1-mer

Ligands

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.1: 37 residues within 4Å: Chain A: K.407, C.432, L.435, C.436, M.594, Q.598, Q.632, E.697, G.698, E.699, N.700, S.704, Q.724, D.725, L.726, F.727, T.729, A.741, S.742, A.743, F.744, K.747, D.774, T.873, R.875, W.880, H.881, T.882, S.884, M.885, F.947, N.955, T.958, F.971, K.972 Ligands: MGD.2, W.3 28 PLIP interactions: 28 interactions with chain A Hydrogen bonds: A:Q.598, A:Q.632, A:N.700, A:N.700, A:S.704, A:S.704, A:Q.724, A:Q.724, A:K.747, A:K.747, A:T.873, A:G.874, A:R.875, A:R.875, A:W.880, A:T.882, A:S.884, A:S.884, A:N.955, A:N.955, A:K.972 Salt bridges: A:E.697, A:D.774, A:H.881, A:H.881 pi-Stacking: A:F.947, A:F.971 pi-Cation interactions: A:F.947 MGD.2: 34 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, F.515, P.517, G.518, D.520, G.593, M.594, G.595, H.599, G.631, Q.632, S.872, T.873, G.874, R.875, V.876, L.877, H.879, W.880, H.881, K.972 Ligands: MGD.1, W.3 21 PLIP interactions: 21 interactions with chain A Hydrogen bonds: A:K.331, A:N.472, A:N.472, A:V.475, A:N.476, A:N.476, A:R.501, A:R.501, A:G.518, A:M.594, A:S.872, A:R.875, A:R.875, A:H.879, A:H.881, 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.3: 3 residues within 4Å: Chain A: C.436 Ligands: MGD.1, MGD.2 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:C.436, H2O.1

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

FES.4: 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.14: 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

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

SF4.5: 12 residues within 4Å: Chain A: C.213, I.214, Q.215, C.216, N.217, 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 SF4.6: 10 residues within 4Å: Chain A: C.223, N.229, V.231, I.232, 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 SF4.7: 9 residues within 4Å: Chain A: C.295, Y.297, C.298, V.300, C.302, C.329, 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 SF4.13: 11 residues within 4Å: Chain B: I.330, S.501, C.502, G.503, Q.504, C.505, C.508, 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

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.8: 5 residues within 4Å: Chain A: K.747, A.748, Q.773, W.775, P.794 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.748, A:A.748 GOL.9: 5 residues within 4Å: Chain A: D.172, V.263, M.272, P.273, R.283 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.283 GOL.11: 5 residues within 4Å: Chain A: D.249, G.253 Chain B: R.22, G.27, R.28 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:D.249, B:R.22, B:R.22 GOL.15: 7 residues within 4Å: Chain B: G.228, G.229, A.230, E.258, G.473, S.474 Ligands: FMN.12 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:G.229, B:E.258, B:S.474 GOL.16: 5 residues within 4Å: Chain B: Y.92, A.93, F.95, D.96, V.97 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:A.93, B:F.95, B:V.97

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.10: 4 residues within 4Å: Chain A: R.684, D.860, A.961, L.962 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.684, A:R.684, A:L.962

1 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.12: 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, L.544 Ligands: GOL.15 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:Y.329, B:Y.329, B:E.333, B:L.544 Hydrogen bonds: B:G.228, B:N.253, B:E.256, B:G.257, B:G.332, B:E.334, B:N.368, B:N.369, B:N.369 Salt bridges: B:K.237

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kobayashi, A. et al., Structure and function relationship of formate dehydrogenases: an overview of recent progress. Iucrj (2023)

Release Date

2023-10-11

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Tungsten-containing formate dehydrogenase alpha subunit

Tungsten-containing formate dehydrogenase beta subunit

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