SMTL ID : 8dyd.1

Crystal structure of human SDHA-SDHAF2-SDHAF4 assembly intermediate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.52 Å

Oligo State

hetero-1-1-1-mer

Ligands

1 x FAD: FLAVIN-ADENINE DINUCLEOTIDE(Covalent)

FAD.1: 42 residues within 4Å: Chain A: V.35, G.36, A.37, G.38, G.39, A.40, G.41, 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, A.409, R.419, A.422, N.423, S.424, L.425, L.428 Chain C: I.96, D.97 Ligands: EDO.23 27 PLIP interactions: 27 interactions with chain A Hydrophobic interactions: A:A.70 Hydrogen bonds: A:A.37, A:A.37, A:G.38, A:G.39, A:A.40, A:K.60, A:K.60, A:L.61, A:H.67, A:T.68, A:T.68, A:G.73, A:G.74, A:G.74, A:A.189, A:D.243, A:E.408, A:A.422, A:S.424, A:S.424, A:L.425 Water bridges: A:G.41, A:G.225, A:E.408, A:E.408 pi-Cation interactions: A:H.375

2 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.2: 6 residues within 4Å: Chain A: L.317, F.494, V.496, E.563, K.566 Ligands: EDO.24 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.563, A:K.566 Water bridges: A:R.320, A:S.498 PG4.3: 12 residues within 4Å: Chain A: F.188, L.190, D.191, L.192, M.194, R.250, A.251, E.459, S.460, N.463, L.534, N.538 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:L.192, A:N.463 Water bridges: A:L.192, A:M.194, A:R.250, A:N.538

1 x K: POTASSIUM ION(Non-covalent)

K.4: 6 residues within 4Å: Chain A: N.377, M.378, G.379, G.380, E.408, A.410 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:N.377, A:G.379, A:E.408, A:A.410, H2O.8

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.5: 4 residues within 4Å: Chain A: A.299, P.300, V.301, A.302 Ligand excluded by PLIP

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

EDO.6: 5 residues within 4Å: Chain A: E.277 Chain C: G.87, D.88, F.98 Ligands: EDO.21 Ligand excluded by PLIP EDO.7: 6 residues within 4Å: Chain A: F.232, Y.269, D.330, K.485, Q.488, N.489 Ligand excluded by PLIP EDO.8: 10 residues within 4Å: Chain A: D.521, W.526, N.527, T.528, D.529 Chain B: A.39, L.42, L.129, L.132, F.133 Ligand excluded by PLIP EDO.9: 9 residues within 4Å: Chain A: L.205, I.207, G.210, M.524, V.525, W.526, N.527, L.530, V.531 Ligand excluded by PLIP EDO.10: 5 residues within 4Å: Chain A: T.316, I.319, L.371, P.372, Q.488 Ligand excluded by PLIP EDO.11: 7 residues within 4Å: Chain A: R.229, H.238, R.480, E.532 Chain B: R.46, K.47, A.126 Ligand excluded by PLIP EDO.12: 5 residues within 4Å: Chain A: K.96, G.97, D.99, N.418, G.558 Ligand excluded by PLIP EDO.13: 4 residues within 4Å: Chain A: R.88, N.618, A.620, D.621 Ligand excluded by PLIP EDO.14: 6 residues within 4Å: Chain A: R.229, F.232, G.270, L.481, Q.484 Chain B: R.125 Ligand excluded by PLIP EDO.15: 5 residues within 4Å: Chain A: Y.548, A.552, V.605, L.607 Ligands: EDO.16 Ligand excluded by PLIP EDO.16: 5 residues within 4Å: Chain A: Q.501, C.504, Y.548, E.551 Ligands: EDO.15 Ligand excluded by PLIP EDO.17: 6 residues within 4Å: Chain A: Y.109, K.386, A.434, L.437, S.438, E.441 Ligand excluded by PLIP EDO.18: 5 residues within 4Å: Chain A: S.508, Y.548, G.603, K.604, V.605 Ligand excluded by PLIP EDO.19: 5 residues within 4Å: Chain A: N.384, L.390, D.397, Q.398, I.399 Ligand excluded by PLIP EDO.20: 3 residues within 4Å: Chain A: N.86, W.89, F.148 Ligand excluded by PLIP EDO.21: 3 residues within 4Å: Chain A: S.307, R.308 Ligands: EDO.6 Ligand excluded by PLIP EDO.22: 5 residues within 4Å: Chain A: F.62, R.65 Chain B: E.44, R.48, N.81 Ligand excluded by PLIP EDO.23: 7 residues within 4Å: Chain A: H.67, G.225, G.226, S.236, S.240, E.408 Ligands: FAD.1 Ligand excluded by PLIP EDO.24: 7 residues within 4Å: Chain A: Y.298, V.310, R.313, S.314, L.317, E.563 Ligands: PG4.2 Ligand excluded by PLIP EDO.25: 5 residues within 4Å: Chain A: G.497, Q.501, K.554, R.562, Y.565 Ligand excluded by PLIP EDO.26: 5 residues within 4Å: Chain A: E.440, E.441, S.442, C.443, R.444 Ligand excluded by PLIP EDO.27: 7 residues within 4Å: Chain A: R.43, A.117, E.120, L.121, Y.124, V.429, R.433 Ligand excluded by PLIP EDO.28: 5 residues within 4Å: Chain A: Y.572, Y.574, I.578, P.626, P.627 Ligand excluded by PLIP EDO.29: 6 residues within 4Å: Chain A: R.313, S.556, A.561, R.562, E.563, K.566 Ligand excluded by PLIP EDO.30: 5 residues within 4Å: Chain A: K.615, T.616, L.617, N.618, E.619 Ligand excluded by PLIP EDO.32: 10 residues within 4Å: Chain A: T.235, G.272, C.273, L.274 Chain B: L.51, E.52, W.87 Chain C: R.94, C.95, I.96 Ligand excluded by PLIP EDO.33: 4 residues within 4Å: Chain B: R.125, A.126, P.127, D.128 Ligand excluded by PLIP EDO.34: 5 residues within 4Å: Chain B: F.60, E.63, H.64, L.110, F.114 Ligand excluded by PLIP EDO.35: 6 residues within 4Å: Chain A: E.353, M.356, I.357 Chain B: T.94, E.95, K.116 Ligand excluded by PLIP EDO.37: 6 residues within 4Å: Chain C: V.68, N.69, P.70, P.78, R.79, G.80 Ligand excluded by PLIP

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

PEG.31: 9 residues within 4Å: Chain A: E.198, C.199, R.200, K.218, N.219, P.401, G.402, C.443, P.450 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:C.199, A:N.219, A:N.219 Water bridges: A:R.200 PEG.36: 5 residues within 4Å: Chain B: E.28, E.70, K.71, N.74, L.75 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.70, B:E.70, B:N.74

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 2, mitochondrial: B
Succinate dehydrogenase assembly factor 4, mitochondrial: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial

Succinate dehydrogenase assembly factor 2, mitochondrial

Succinate dehydrogenase assembly factor 4, mitochondrial

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