SMTL ID : 8w0z.2 (1 other biounit)

Human LCAD complexed with Lauric Acid

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-tetramer

Ligands

4 x FAD: FLAVIN-ADENINE DINUCLEOTIDE(Non-covalent)

FAD.1: 31 residues within 4Å: Chain A: I.140, A.141, M.142, T.143, A.147, G.148, S.149, F.173, I.174, S.175, K.220, V.377, I.380, Y.381, G.382, T.384, E.386, I.387, E.390 Chain B: R.287, F.290, V.294, L.297, T.299, Q.355, L.356, G.358, G.359 Chain C: Q.298, H.302 Ligands: DAO.2 26 PLIP interactions: 1 interactions with chain C, 19 interactions with chain A, 6 interactions with chain B Hydrogen bonds: C:Q.298, A:I.140, A:M.142, A:T.143, A:T.143, A:G.148, A:S.149, A:S.149, A:S.175, A:G.382, A:T.384, A:T.384, A:E.390, B:Q.355, B:G.359 Hydrophobic interactions: A:F.173, A:K.220, A:V.377, A:Y.381 Water bridges: A:E.144, A:T.384, B:R.287, B:T.299 pi-Stacking: A:Y.381 Salt bridges: B:R.287, B:R.287 FAD.3: 28 residues within 4Å: Chain A: R.287, F.290, V.294, L.297, T.299, Q.355, L.356, G.358, G.359 Chain B: I.140, A.141, M.142, T.143, G.148, S.149, F.173, I.174, S.175, K.220, V.377, I.380, Y.381, G.382, T.384, E.386, I.387 Chain D: Q.298 Ligands: DAO.4 24 PLIP interactions: 17 interactions with chain B, 1 interactions with chain D, 6 interactions with chain A Hydrophobic interactions: B:F.173, B:K.220, B:V.377, B:Y.381 Hydrogen bonds: B:I.140, B:M.142, B:T.143, B:T.143, B:G.148, B:S.149, B:S.149, B:S.175, B:G.382, B:T.384, B:E.390, D:Q.298, A:Q.355, A:G.359 Water bridges: B:T.384, A:R.287, A:R.287 pi-Stacking: B:Y.381 Salt bridges: A:R.287, A:R.287 FAD.5: 28 residues within 4Å: Chain A: Q.298 Chain C: I.140, A.141, M.142, T.143, G.148, S.149, F.173, I.174, S.175, V.377, I.380, Y.381, G.382, T.384, E.386, I.387, E.390 Chain D: R.287, F.290, V.294, L.297, T.299, Q.355, L.356, G.358, G.359 Ligands: DAO.6 26 PLIP interactions: 20 interactions with chain C, 5 interactions with chain D, 1 interactions with chain A Hydrophobic interactions: C:F.173, C:V.377, C:Y.381 Hydrogen bonds: C:I.140, C:M.142, C:T.143, C:T.143, C:S.149, C:S.149, C:S.175, C:G.382, C:T.384, C:T.384, C:E.386, C:E.390, D:Q.355, D:G.359, A:Q.298 Water bridges: C:E.144, C:G.148, C:D.150, C:T.384, D:R.287 pi-Stacking: C:Y.381 Salt bridges: D:R.287, D:R.287 FAD.7: 30 residues within 4Å: Chain B: Q.298, H.302 Chain C: R.287, F.290, V.294, L.297, T.299, Q.355, L.356, G.358, G.359 Chain D: I.140, A.141, M.142, T.143, G.148, S.149, F.173, I.174, S.175, K.220, V.377, I.380, Y.381, G.382, T.384, E.386, I.387, E.390 Ligands: DAO.8 27 PLIP interactions: 1 interactions with chain B, 20 interactions with chain D, 6 interactions with chain C Hydrogen bonds: B:Q.298, D:I.140, D:M.142, D:T.143, D:T.143, D:G.148, D:S.149, D:S.149, D:S.175, D:G.382, D:T.384, D:E.390, D:E.390, C:Q.355, C:G.359 Hydrophobic interactions: D:F.173, D:K.220, D:V.377, D:Y.381 Water bridges: D:I.140, D:D.150, D:T.384, C:R.287, C:R.287 pi-Stacking: D:Y.381 Salt bridges: C:R.287, C:R.287

4 x DAO: LAURIC ACID(Non-covalent)

DAO.2: 7 residues within 4Å: Chain A: S.105, I.106, Q.261, I.265, Y.381, G.382 Ligands: FAD.1 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:I.106, A:I.106, A:I.265, A:I.265 Hydrogen bonds: A:Q.261, A:Q.261, A:G.382 DAO.4: 7 residues within 4Å: Chain B: I.106, M.142, Q.261, I.265, Y.381, G.382 Ligands: FAD.3 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:I.106, B:I.106, B:I.265, B:I.265 Hydrogen bonds: B:Q.261, B:G.382 Water bridges: B:T.143, B:T.143 DAO.6: 8 residues within 4Å: Chain C: S.105, I.106, Q.261, L.264, I.265, Y.381, G.382 Ligands: FAD.5 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:I.106, C:I.106, C:I.265, C:I.265 Hydrogen bonds: C:G.382 Water bridges: C:Q.261, C:Q.261 DAO.8: 8 residues within 4Å: Chain D: S.105, I.106, M.142, Q.261, L.264, I.265, Y.381 Ligands: FAD.7 7 PLIP interactions: 7 interactions with chain D Hydrophobic interactions: D:I.106, D:I.106, D:L.264, D:I.265, D:I.265 Hydrogen bonds: D:Q.261, D:G.382

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Narayanan, B. et al., Structural basis for expanded substrate specificities of human long chain acyl-CoA dehydrogenase and related acyl-CoA dehydrogenases. Sci Rep (2024)

Release Date

2024-06-19

Peptides

Long-chain specific acyl-CoA dehydrogenase, mitochondrial: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
E

B
F

C
G

D
H

Long-chain specific acyl-CoA dehydrogenase, mitochondrial

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