SMTL ID : 7qh2.1

Cryo-EM structure of Ldh-EtfAB complex from Acetobacterium woodii

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-2-2-mer

Ligands

6 x FAD: FLAVIN-ADENINE DINUCLEOTIDE(Non-covalent)

FAD.1: 31 residues within 4Å: Chain A: G.284, R.285, G.286, K.288, T.310, R.311, P.312, Q.324, I.325, G.326, L.327, S.328, G.329, G.341, I.342, S.343, A.345, Q.347, F.348, N.362, S.363, D.364, G.379, D.380, L.381, Y.382 Chain C: D.32, E.37, T.78, E.139 Ligands: FAD.3 20 PLIP interactions: 20 interactions with chain A Hydrophobic interactions: A:Q.347 Hydrogen bonds: A:R.285, A:R.285, A:K.288, A:T.310, A:T.310, A:R.311, A:I.325, A:S.328, A:G.329, A:S.343, A:Q.347, A:N.362, A:S.363, A:D.364, A:D.380, A:L.381 Salt bridges: A:R.285, A:R.285 pi-Cation interactions: A:R.311 FAD.2: 30 residues within 4Å: Chain A: L.186, T.187, A.188, R.205, A.207, I.216 Chain B: C.7, I.8, K.9, N.36, D.39, S.61, M.62, A.93, D.94, V.95, T.98, L.102, C.117, G.118, Q.120, T.121, D.123, G.124, D.125, T.126, A.127, Q.128, V.129, T.226 25 PLIP interactions: 21 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:N.36, B:D.39, B:M.62, B:M.62, B:A.93, B:V.95, B:T.98, B:G.118, B:Q.120, B:T.121, B:G.124, B:D.125, B:T.126, B:T.126, B:T.126, B:A.127, B:Q.128, B:Q.128, B:V.129, B:T.226, A:L.186, A:A.188, A:R.205 Salt bridges: B:K.9 Hydrophobic interactions: A:A.207 FAD.3: 33 residues within 4Å: Chain C: E.37, V.73, R.74, G.75, S.76, G.77, T.78, G.79, L.80, A.83, C.84, P.115, P.137, G.138, E.139, A.142, T.143, A.145, G.146, N.147, S.149, T.150, A.152, G.153, E.203, G.204, C.207, V.208, I.209, L.332, E.422, H.423 Ligands: FAD.1 25 PLIP interactions: 25 interactions with chain C Hydrophobic interactions: C:E.37, C:L.80, C:L.80, C:E.139, C:L.332 Hydrogen bonds: C:V.73, C:G.75, C:S.76, C:G.77, C:T.78, C:T.78, C:G.79, C:G.138, C:E.139, C:T.143, C:N.147, C:S.149, C:T.150, C:G.153, C:G.153, C:I.209, C:I.209, C:N.459 pi-Stacking: C:H.423, C:H.423 FAD.5: 30 residues within 4Å: Chain D: G.284, R.285, G.286, K.288, T.310, R.311, P.312, Q.324, I.325, G.326, L.327, S.328, G.329, G.341, I.342, S.343, A.345, Q.347, F.348, N.362, S.363, D.364, G.379, D.380, L.381, Y.382 Chain F: D.32, E.37, E.139 Ligands: FAD.7 20 PLIP interactions: 20 interactions with chain D Hydrophobic interactions: D:Q.347 Hydrogen bonds: D:R.285, D:R.285, D:K.288, D:T.310, D:T.310, D:R.311, D:I.325, D:S.328, D:G.329, D:S.343, D:Q.347, D:N.362, D:S.363, D:D.364, D:D.380, D:L.381 Salt bridges: D:R.285, D:R.285 pi-Cation interactions: D:R.311 FAD.6: 30 residues within 4Å: Chain D: L.186, T.187, A.188, R.205, A.207, I.216 Chain E: C.7, I.8, K.9, N.36, D.39, S.61, M.62, A.93, D.94, V.95, T.98, L.102, C.117, G.118, Q.120, T.121, D.123, G.124, D.125, T.126, A.127, Q.128, V.129, T.226 25 PLIP interactions: 21 interactions with chain E, 4 interactions with chain D Hydrogen bonds: E:N.36, E:D.39, E:M.62, E:M.62, E:A.93, E:V.95, E:T.98, E:G.118, E:Q.120, E:T.121, E:G.124, E:D.125, E:T.126, E:T.126, E:T.126, E:A.127, E:Q.128, E:Q.128, E:V.129, E:T.226, D:L.186, D:A.188, D:R.205 Salt bridges: E:K.9 Hydrophobic interactions: D:A.207 FAD.7: 33 residues within 4Å: Chain F: E.37, V.73, R.74, G.75, S.76, G.77, T.78, G.79, L.80, A.83, C.84, P.115, P.137, G.138, E.139, A.142, T.143, A.145, G.146, N.147, S.149, T.150, A.152, G.153, E.203, G.204, C.207, V.208, I.209, L.332, E.422, H.423 Ligands: FAD.5 24 PLIP interactions: 24 interactions with chain F Hydrophobic interactions: F:E.37, F:L.80, F:E.139, F:L.332 Hydrogen bonds: F:V.73, F:G.75, F:S.76, F:G.77, F:T.78, F:T.78, F:G.79, F:G.138, F:E.139, F:T.143, F:N.147, F:S.149, F:T.150, F:G.153, F:G.153, F:I.209, F:I.209, F:N.459 pi-Stacking: F:H.423, F:H.423

2 x FE: FE (III) ION(Non-covalent)

FE.4: 4 residues within 4Å: Chain C: H.377, N.382, H.384, E.422 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:H.377, C:H.384, C:E.422, C:E.422, H2O.1 FE.8: 4 residues within 4Å: Chain F: H.377, N.382, H.384, E.422 5 PLIP interactions: 4 interactions with chain F, 1 Ligand-Water interactions Metal complexes: F:H.377, F:H.384, F:E.422, F:E.422, H2O.1

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kayastha, K. et al., Structure-based electron-confurcation mechanism of the Ldh-EtfAB complex. Elife (2022)

Release Date

2022-06-29

Peptides

Lactate dehydrogenase (NAD(+),ferredoxin) subunit LctC: AD
Lactate dehydrogenase (NAD(+),ferredoxin) subunit LctB: BE
Lactate dehydrogenase (NAD(+),ferredoxin) subunit LctD: CF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

D
D

B
B

E
E

C
C

F
F

Lactate dehydrogenase (NAD(+),ferredoxin) subunit LctC

Lactate dehydrogenase (NAD(+),ferredoxin) subunit LctB

Lactate dehydrogenase (NAD(+),ferredoxin) subunit LctD