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

Crystal structure of human SDHA-ADHAF2 assembly intermediate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.59 Å

Oligo State

hetero-1-1-mer

Ligands

1 x FAD: FLAVIN-ADENINE DINUCLEOTIDE(Covalent)

FAD.1: 38 residues within 4Å: Chain A: V.35, G.36, A.37, G.38, G.39, A.40, V.58, T.59, K.60, L.61, S.66, H.67, T.68, A.70, A.71, Q.72, G.73, G.74, Y.187, F.188, A.189, A.223, T.224, G.225, T.235, S.236, D.243, H.375, Y.376, G.407, E.408, R.419, A.422, N.423, S.424, L.425, L.428 Ligands: OAA.2 28 PLIP interactions: 28 interactions with chain A Hydrophobic interactions: A:A.70 Hydrogen bonds: A:A.37, A:G.38, A:G.39, A:A.40, A:K.60, A:K.60, A:L.61, A:S.66, A:H.67, A:T.68, A:T.68, A:Q.72, A:G.73, A:G.74, A:G.74, A:A.189, A:A.189, A:G.225, A:E.408, A:R.419, A:A.422, A:S.424, A:L.425 Water bridges: A:G.41, A:E.408, A:E.408 pi-Stacking: A:H.375

1 x OAA: OXALOACETATE ION(Non-covalent)

OAA.2: 9 residues within 4Å: Chain A: F.141, H.264, L.274, R.308, H.375, R.419, G.421, A.422 Ligands: FAD.1 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:L.274 Hydrogen bonds: A:R.308, A:R.308, A:R.419, A:A.422 Salt bridges: A:H.264, A:R.308, A:H.375, A:R.419

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

MLI.3: 6 residues within 4Å: Chain A: E.571, H.589, R.591, P.611, V.612, D.614 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:V.612, A:D.614 Salt bridges: A:K.583, A:H.589, A:H.589, A:R.591, A:R.591

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 6 residues within 4Å: Chain A: Q.262, F.263, D.309, R.313, V.493, A.559 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:F.263, A:D.309

1 x K: POTASSIUM ION(Non-covalent)

K.5: 5 residues within 4Å: Chain A: N.377, M.378, G.379, E.408, A.410 6 PLIP interactions: 5 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:N.377, A:M.378, A:G.379, A:E.408, A:A.410, H2O.1

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

EDO.6: 7 residues within 4Å: Chain A: D.99, S.556, R.557, G.558, R.568, R.630, Y.632 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.99, A:G.558, A:R.630, A:Y.632 EDO.7: 6 residues within 4Å: Chain A: R.568, I.569, D.570, Y.572, D.573, K.584 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.568, A:D.570 EDO.8: 2 residues within 4Å: Chain A: Q.501, E.551 No protein-ligand interaction detected (PLIP) EDO.9: 3 residues within 4Å: Chain A: Y.597, T.606, E.608 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sharma, P. et al., The roles of SDHAF2 and dicarboxylate in covalent flavinylation of SDHA, the human complex II flavoprotein. Proc.Natl.Acad.Sci.USA (2020)

Release Date

2020-08-26

Peptides

Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial: A
Succinate dehydrogenase assembly factor 2, mitochondrial: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial

Succinate dehydrogenase assembly factor 2, mitochondrial

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