SMTL ID : 8w0u.1

Human LCAD complexed with Acetoacetyl Coenzyme A

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

homo-tetramer

Ligands

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

FAD.1: 27 residues within 4Å: Chain A: 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, G.383, T.384, E.386, I.387 Chain B: R.287, F.290, L.297, T.299, Q.355, L.356, G.358, G.359 Chain C: Q.298 Ligands: CAA.2 18 PLIP interactions: 14 interactions with chain A, 3 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: A:F.173, A:V.377, A:Y.381 Hydrogen bonds: A:I.140, A:M.142, A:T.143, A:T.143, A:S.149, A:S.175, A:G.382, A:G.383, A:T.384, A:T.384, B:L.356, B:G.359, C:Q.298 pi-Stacking: A:Y.381 Salt bridges: B:R.287 FAD.3: 27 residues within 4Å: Chain A: R.287, F.290, 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, T.228, V.377, I.380, Y.381, G.383, T.384, E.386, I.387 Chain D: Q.298 Ligands: CAA.4 20 PLIP interactions: 6 interactions with chain A, 1 interactions with chain D, 13 interactions with chain B Hydrogen bonds: A:L.356, A:G.359, D:Q.298, B:I.140, B:M.142, B:T.143, B:T.143, B:S.149, B:S.149, B:S.175, B:G.383, B:T.384 Water bridges: A:R.287, A:R.287, B:T.384 Salt bridges: A:R.287, A:R.287 Hydrophobic interactions: B:F.173, B:Y.381 pi-Stacking: B:Y.381 FAD.5: 31 residues within 4Å: Chain A: Q.298 Chain C: I.140, A.141, M.142, T.143, G.148, S.149, F.173, S.175, K.220, L.223, V.377, I.380, Y.381, G.382, G.383, T.384, E.386, I.387, E.390 Chain D: R.287, F.290, L.297, T.299, Q.355, L.356, H.357, G.358, G.359, W.360, Y.362 24 PLIP interactions: 18 interactions with chain C, 5 interactions with chain D, 1 interactions with chain A Hydrophobic interactions: C:F.173, C:K.220, C:L.223, C:V.377, C:Y.381, C:Y.381, D:Y.362 Hydrogen bonds: C:I.140, C:M.142, C:T.143, C:T.143, C:S.149, C:S.175, C:G.382, C:G.383, C:T.384, C:T.384, C:E.386, C:E.390, D:L.356, D:G.359, D:W.360, A:Q.298 Salt bridges: D:R.287 FAD.6: 33 residues within 4Å: Chain B: Q.298 Chain C: Y.283, R.287, F.290, V.294, L.297, T.299, Q.355, L.356, H.357, G.358, G.359 Chain D: I.140, A.141, M.142, T.143, A.147, G.148, S.149, F.173, I.174, S.175, L.223, T.228, V.377, I.380, Y.381, G.382, G.383, T.384, E.386, I.387, E.390 25 PLIP interactions: 6 interactions with chain C, 18 interactions with chain D, 1 interactions with chain B Hydrogen bonds: C:Y.283, C:Y.283, C:Q.355, C:G.359, 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:G.383, D:T.384, D:E.390, D:E.390, B:Q.298 Salt bridges: C:R.287, C:R.287 Hydrophobic interactions: D:F.173, D:L.223, D:V.377, D:Y.381 pi-Stacking: D:Y.381

2 x CAA: ACETOACETYL-COENZYME A(Non-covalent)

CAA.2: 21 residues within 4Å: Chain A: I.106, M.142, G.148, S.149, L.151, Q.152, S.195, H.198, F.251, Y.252, M.255, L.258, E.261, R.262, Y.381, G.382, G.383, I.387, L.391, R.394 Ligands: FAD.1 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:E.261, A:Y.381, A:L.391 Hydrogen bonds: A:S.149, A:L.151, A:Q.152, A:S.195, A:Y.252, A:R.262, A:G.382 Salt bridges: A:H.198, A:R.394, A:R.394 pi-Stacking: A:Y.252 CAA.4: 21 residues within 4Å: Chain A: F.290 Chain B: I.106, M.142, G.148, S.149, L.151, Q.152, S.195, H.198, Y.252, M.255, L.258, E.261, R.262, Y.381, G.382, G.383, I.387, L.391, R.394 Ligands: FAD.3 16 PLIP interactions: 15 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:I.106, B:E.261, B:L.391, A:F.290 Hydrogen bonds: B:S.149, B:L.151, B:Q.152, B:S.195, B:S.195, B:R.262, B:G.382 Salt bridges: B:H.198, B:R.394, B:R.394 pi-Stacking: B:Y.252, B:Y.252

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
A

B
B

C
C

D
D

Long-chain specific acyl-CoA dehydrogenase, mitochondrial

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