SMTL ID : 7e5z.1

Dehydrogenase holoenzyme

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-mer

Ligands

1 x W: TUNGSTEN ION(Non-covalent)

W.1: 3 residues within 4Å: Chain A: C.436 Ligands: MGD.2, MGD.3 No protein-ligand interaction detected (PLIP)

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.2: 20 residues within 4Å: Chain A: K.407, G.408, C.436, Q.632, E.697, G.698, E.699, N.700, M.703, S.704, D.725, L.726, T.729, A.741, S.742, F.744, K.747, D.774 Ligands: W.1, MGD.3 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:K.407, A:Q.632, A:N.700, A:M.703, A:S.704, A:D.725 Salt bridges: A:K.407, A:D.774 MGD.3: 22 residues within 4Å: Chain A: C.436, I.469, G.470, A.471, N.472, V.475, N.476, H.477, D.499, P.500, F.515, P.517, G.518, G.593, M.594, G.595, V.596, R.630, G.631, Q.632 Ligands: W.1, MGD.2 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:A.471, A:A.471, A:N.472, A:N.476, A:D.520, A:D.520, A:M.594 Salt bridges: A:D.499

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

FES.4: 11 residues within 4Å: Chain A: H.100, C.102, H.103, G.113, N.114, C.115, R.116, A.117, C.118, A.130, 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.10: 10 residues within 4Å: Chain B: C.113, T.117, C.118, C.146, V.147, G.148, L.149, C.150, A.155, P.259 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(Covalent)(Non-covalent)

SF4.5: 14 residues within 4Å: Chain A: L.210, A.212, C.213, I.214, Q.215, C.216, N.217, L.218, C.219, V.243, C.266, P.267, T.268, 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: 14 residues within 4Å: Chain A: M.206, C.223, Q.227, N.229, V.231, I.232, F.245, C.256, V.257, A.258, C.259, G.260, E.261, C.262 7 PLIP interactions: 7 interactions with chain A, Metal complexes: A:C.223, A:C.223, A:C.256, A:C.259, A:C.259, A:C.259, A:C.262 SF4.7: 12 residues within 4Å: Chain A: C.295, Y.297, C.298, V.300, G.301, C.302, N.324, L.328, C.329, K.331, P.478, V.479 5 PLIP interactions: 5 interactions with chain A, Metal complexes: A:C.295, A:C.295, A:C.298, A:C.302, A:C.329 SF4.9: 12 residues within 4Å: Chain B: P.348, S.501, C.502, G.503, Q.504, C.505, C.508, R.509, S.540, C.542, L.544, G.545 7 PLIP interactions: 7 interactions with chain B, Metal complexes: B:C.502, B:C.502, B:C.505, B:C.508, B:C.508, B:C.542, B:C.542

1 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.8: 20 residues within 4Å: Chain B: G.226, L.227, G.228, G.229, A.230, 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 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:E.333, B:L.544 Hydrogen bonds: B:L.227, B:N.253, B:N.253, B:E.256, B:G.257, B:G.332, B:E.334, B:E.334, B:N.368, B:N.369 Salt bridges: B:K.237

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Roh, S.H. et al., Dehydrogenase holoenzyme. To Be Published

Release Date

2022-02-23

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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