SMTL ID : 6b58.1 (1 other biounit)

FrdA-SdhE assembly intermediate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.61 Å

Oligo State

hetero-1-1-mer

Ligands

1 x FAD: FLAVIN-ADENINE DINUCLEOTIDE(Covalent)

FAD.1: 36 residues within 4Å: Chain A: G.12, A.13, G.14, G.15, A.16, I.36, S.37, K.38, V.39, S.44, H.45, T.46, A.48, A.49, E.50, H.156, F.157, V.158, A.192, T.193, G.194, T.204, N.205, D.212, M.216, H.356, Y.357, G.379, E.380, R.391, G.393, S.394, S.396, L.397, L.400 Ligands: ACT.9 22 PLIP interactions: 22 interactions with chain A Hydrophobic interactions: A:A.48 Hydrogen bonds: A:A.13, A:A.13, A:A.16, A:K.38, A:K.38, A:V.39, A:H.45, A:T.46, A:T.46, A:E.50, A:V.158, A:V.158, A:E.380, A:R.391, A:S.394, A:S.396, A:S.396, A:L.397 Water bridges: A:G.194, A:G.194 pi-Cation interactions: A:H.356

1 x K: POTASSIUM ION(Non-covalent)

K.2: 6 residues within 4Å: Chain A: Y.357, T.358, M.359, G.360, E.380, S.382 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:T.358, A:E.380

7 x ACT: ACETATE ION(Non-functional Binders)

ACT.3: 3 residues within 4Å: Chain A: Y.85, N.367, L.406 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:Y.85 Hydrogen bonds: A:N.367 ACT.4: 2 residues within 4Å: Chain A: Q.146, F.147 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.146 ACT.5: 3 residues within 4Å: Chain A: L.549, D.568, V.569 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.549 Hydrogen bonds: A:L.549, A:D.568, A:V.569 ACT.6: 5 residues within 4Å: Chain A: E.64, F.67, D.84, H.88, T.573 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.67 Hydrogen bonds: A:D.84 ACT.7: 5 residues within 4Å: Chain A: G.73, R.288, N.390, R.391, L.392 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.392 Hydrogen bonds: A:N.390 Salt bridges: A:R.288 ACT.8: 5 residues within 4Å: Chain A: E.538, G.539, C.540, T.541, E.542 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:T.541 Hydrogen bonds: A:G.539, A:T.541 ACT.9: 4 residues within 4Å: Chain A: H.233, H.356, R.391 Ligands: FAD.1 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:H.356, A:R.391

4 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.10: 5 residues within 4Å: Chain A: R.19, A.23, Q.26, R.405, E.409 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.19, A:R.19, A:Q.26, A:R.405 EDO.11: 4 residues within 4Å: Chain A: W.299, R.300, T.469, L.472 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.300 EDO.12: 3 residues within 4Å: Chain A: S.219, H.511, N.514 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.219, A:S.219, A:N.514 EDO.13: 4 residues within 4Å: Chain A: L.392, G.393, S.394, N.395 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.394

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sharma, P. et al., Crystal structure of an assembly intermediate of respiratory Complex II. Nat Commun (2018)

Release Date

2018-01-24

Peptides

Fumarate reductase flavoprotein subunit: A
FAD assembly factor SdhE: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Fumarate reductase flavoprotein subunit

FAD assembly factor SdhE

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