SMTL ID : 6b58.2 (1 other biounit)

FrdA-SdhE assembly intermediate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.61 Å

Oligo State

hetero-1-1-mer

Ligands

1 x FAD: FLAVIN-ADENINE DINUCLEOTIDE(Covalent)

FAD.1: 35 residues within 4Å: Chain A: G.12, A.13, G.14, G.15, A.16, S.37, K.38, V.39, S.44, H.45, T.46, A.48, A.49, E.50, G.51, H.156, F.157, V.158, A.192, T.193, G.194, T.204, N.205, D.212, H.356, Y.357, G.379, E.380, R.391, G.393, S.394, S.396, L.397, L.400 Ligands: MLI.4 23 PLIP interactions: 23 interactions with chain A Hydrophobic interactions: A:A.48 Hydrogen bonds: A:A.13, A:A.13, A:G.14, 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:G.51, A:V.158, A:V.158, A:G.194, A:D.212, A:E.380, A:E.380, A:S.396, A:L.397 Water bridges: A:G.17 pi-Cation interactions: A:H.356

1 x K: POTASSIUM ION(Non-covalent)

K.2: 5 residues within 4Å: Chain A: T.358, M.359, G.360, E.380, S.382 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:T.358, A:G.360, A:E.380, A:S.382

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

PEG.3: 8 residues within 4Å: Chain A: L.159, D.160, M.216, S.219, R.436, I.507, G.510, H.511 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:L.159, A:S.219, A:I.507

1 x MLI: MALONATE ION(Non-functional Binders)

MLI.4: 6 residues within 4Å: Chain A: G.51, R.288, H.356, R.391, G.393 Ligands: FAD.1 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:G.393 Salt bridges: A:R.288, A:R.288, A:H.356, A:R.391

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 4 residues within 4Å: Chain A: L.145, P.148, I.150, R.152 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:L.145, A:P.148, A:R.152

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

ACT.6: 2 residues within 4Å: Chain A: Q.5, D.7 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.7 Salt bridges: A:K.32 ACT.7: 1 residues within 4Å: Chain A: N.367 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.367 ACT.8: 5 residues within 4Å: Chain A: Y.267, K.290, Q.293, H.297, Y.467 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.293 Salt bridges: A:K.290 ACT.9: 5 residues within 4Å: Chain A: F.63, E.64, F.67, D.84, H.88 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:F.63, A:E.64 Salt bridges: A:H.88

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
C

B
D

Fumarate reductase flavoprotein subunit

FAD assembly factor SdhE

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