SMTL ID : 8dye.1

Crystal structure of human SDHA-SDHAF4 assembly intermediate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.44 Å

Oligo State

hetero-1-1-mer

Ligands

1 x FAD: FLAVIN-ADENINE DINUCLEOTIDE(Covalent)

FAD.1: 42 residues within 4Å: Chain A: V.14, G.15, A.16, G.17, G.18, A.19, G.20, V.37, T.38, K.39, L.40, S.45, H.46, T.47, A.49, A.50, G.52, G.53, Y.166, F.167, A.168, A.202, T.203, G.204, T.214, S.215, D.222, H.354, Y.355, G.386, E.387, A.388, R.398, A.401, N.402, S.403, L.404, L.407 Chain B: I.96, D.97 Ligands: EDO.3, NA.23 31 PLIP interactions: 30 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:A.49 Hydrogen bonds: A:A.16, A:A.16, A:G.17, A:A.19, A:K.39, A:K.39, A:L.40, A:H.46, A:T.47, A:T.47, A:G.52, A:G.53, A:G.53, A:A.168, A:G.204, A:D.222, A:D.222, A:E.387, A:E.387, A:R.398, A:A.401, A:S.403, A:S.403, A:L.404, B:D.97 Water bridges: A:D.222, A:E.387, A:E.387, A:A.388 pi-Cation interactions: A:H.354

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

MLI.2: 9 residues within 4Å: Chain A: D.78, S.535, R.536, G.537, K.545, V.546, R.547, R.609, Y.611 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:G.537, A:R.547, A:Y.611 Water bridges: A:R.609, A:R.609 Salt bridges: A:R.609

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

EDO.3: 7 residues within 4Å: Chain A: H.46, G.204, G.205, S.215, S.219, E.387 Ligands: FAD.1 Ligand excluded by PLIP EDO.4: 7 residues within 4Å: Chain A: R.208, F.211, S.212, C.213, G.249, A.250, G.251 Ligand excluded by PLIP EDO.5: 5 residues within 4Å: Chain A: S.487, Y.527, K.583, V.584 Ligands: EDO.17 Ligand excluded by PLIP EDO.6: 8 residues within 4Å: Chain A: D.170, R.229, E.438, S.439, N.442, V.579 Ligands: EDO.13, GOL.16 Ligand excluded by PLIP EDO.8: 4 residues within 4Å: Chain A: N.363, L.369, D.376, I.378 Ligand excluded by PLIP EDO.9: 6 residues within 4Å: Chain A: S.28, G.31, F.32, N.33, Y.158, D.159 Ligand excluded by PLIP EDO.10: 4 residues within 4Å: Chain A: R.67, N.597, A.599, D.600 Ligand excluded by PLIP EDO.12: 5 residues within 4Å: Chain A: Y.490, L.493, Q.516, V.579 Ligands: GOL.16 Ligand excluded by PLIP EDO.13: 5 residues within 4Å: Chain A: D.170, R.229, A.230, E.438 Ligands: EDO.6 Ligand excluded by PLIP EDO.14: 6 residues within 4Å: Chain A: T.228, R.229, G.231, V.577, D.578, V.579 Ligand excluded by PLIP EDO.15: 3 residues within 4Å: Chain A: N.65, W.68, F.127 Ligand excluded by PLIP EDO.17: 4 residues within 4Å: Chain A: Y.527, V.584, L.586 Ligands: EDO.5 Ligand excluded by PLIP EDO.18: 10 residues within 4Å: Chain A: Y.2, L.184, G.189, I.191, L.443, R.447, G.502, M.503, N.506, L.509 Ligand excluded by PLIP EDO.19: 4 residues within 4Å: Chain A: D.593, K.594, E.598, T.603 Ligand excluded by PLIP EDO.20: 4 residues within 4Å: Chain A: Q.480, C.483, Y.527, E.530 Ligand excluded by PLIP EDO.21: 6 residues within 4Å: Chain A: K.197, N.198, P.380, G.381, S.421, C.422 Ligand excluded by PLIP

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 6 residues within 4Å: Chain A: F.211, Y.248, D.309, K.464, Q.467, N.468 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.309, A:N.468, A:N.468 GOL.11: 9 residues within 4Å: Chain A: R.22, F.25, G.26, E.29, Y.103, R.412, A.415, L.416, E.419 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:R.22, A:R.22, A:Y.103, A:E.419 Water bridges: A:E.29, A:E.29, A:R.412 GOL.16: 7 residues within 4Å: Chain A: R.229, N.442, Q.516, L.520, V.579 Ligands: EDO.6, EDO.12 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.229 Water bridges: A:L.169, A:D.170, A:R.229, A:N.442, A:Q.516

2 x NA: SODIUM ION(Non-functional Binders)

NA.22: 6 residues within 4Å: Chain A: N.356, M.357, G.358, G.359, E.387, A.389 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:A.389 NA.23: 7 residues within 4Å: Chain A: G.15, A.16, G.17, A.19, G.20, A.202 Ligands: FAD.1 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.17, A:A.19, A:G.20, A:A.202

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sharma, P. et al., Disordered-to-ordered transitions in assembly factors allow the complex II catalytic subunit to switch binding partners. Nat Commun (2024)

Release Date

2024-01-10

Peptides

Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial: A
Succinate dehydrogenase assembly factor 4, mitochondrial: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial

Succinate dehydrogenase assembly factor 4, mitochondrial

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