SMTL ID : 6sda.1

Bd2924 C10 acyl-coenzymeA bound form

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.87 Å

Oligo State

homo-tetramer

Ligands

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

FAD.1: 33 residues within 4Å: Chain A: M.134, Q.171, W.172, M.173, T.174, G.178, G.179, S.180, F.210, T.211, S.212, K.260, T.263, T.268, V.424, I.427, W.428, E.429, T.431, N.433, V.434, L.437 Chain B: R.324, A.326, F.327, L.331, H.334, H.337, E.402, M.403, G.405, G.406, Y.409 29 PLIP interactions: 11 interactions with chain B, 18 interactions with chain A Hydrophobic interactions: B:Y.409, B:Y.409, A:F.210, A:K.260, A:T.268, A:V.424 Hydrogen bonds: B:M.403, B:G.406, A:Q.171, A:M.173, A:T.174, A:T.174, A:T.174, A:G.179, A:S.180, A:S.180, A:E.429, A:T.431, A:T.431 Water bridges: B:Y.320, B:R.324, B:H.337, B:H.337, B:A.407, A:S.212, A:S.212 Salt bridges: B:R.324, B:R.324 pi-Stacking: A:W.428 FAD.3: 32 residues within 4Å: Chain A: R.324, A.326, F.327, L.331, H.334, H.337, E.402, M.403, G.405, G.406, Y.409 Chain B: Q.171, W.172, M.173, T.174, G.178, G.179, S.180, F.210, T.211, S.212, K.260, T.268, V.424, I.427, W.428, E.429, T.431, N.433, V.434, L.437 Ligands: MFK.2 37 PLIP interactions: 13 interactions with chain A, 24 interactions with chain B Hydrophobic interactions: A:Y.409, A:Y.409, B:F.210, B:K.260, B:T.268, B:V.424, B:W.428 Hydrogen bonds: A:H.334, A:E.402, A:G.406, B:Q.171, B:M.173, B:T.174, B:T.174, B:T.174, B:G.179, B:S.180, B:S.180, B:E.429, B:T.431, B:N.433, B:V.434 Water bridges: A:Y.320, A:R.324, A:A.407, A:A.407, B:T.174, B:G.178, B:F.210, B:S.212, B:S.212, B:T.431, B:T.432 Salt bridges: A:R.324, A:R.324 pi-Stacking: A:H.334, A:H.334 FAD.4: 33 residues within 4Å: Chain C: M.134, Q.171, W.172, M.173, T.174, G.178, G.179, S.180, F.210, T.211, S.212, K.260, T.263, T.268, V.424, I.427, W.428, E.429, T.431, N.433, V.434, L.437 Chain D: R.324, A.326, F.327, L.331, H.334, H.337, E.402, M.403, G.405, G.406, Y.409 26 PLIP interactions: 18 interactions with chain C, 8 interactions with chain D Hydrophobic interactions: C:F.210, C:K.260, C:T.268, C:V.424, D:Y.409, D:Y.409 Hydrogen bonds: C:Q.171, C:M.173, C:T.174, C:T.174, C:T.174, C:G.179, C:S.180, C:S.180, C:E.429, C:T.431, D:M.403, D:G.406 Water bridges: C:S.212, C:S.212, C:N.433, D:R.324, D:A.407 pi-Stacking: C:W.428 Salt bridges: D:R.324, D:R.324 FAD.6: 32 residues within 4Å: Chain C: R.324, A.326, F.327, L.331, H.334, H.337, E.402, M.403, G.405, G.406, Y.409 Chain D: Q.171, W.172, M.173, T.174, G.178, G.179, S.180, F.210, T.211, S.212, K.260, T.268, V.424, I.427, W.428, E.429, T.431, N.433, V.434, L.437 Ligands: MFK.5 40 PLIP interactions: 23 interactions with chain D, 17 interactions with chain C Hydrophobic interactions: D:F.210, D:K.260, D:T.268, D:V.424, D:W.428, C:Y.409, C:Y.409 Hydrogen bonds: D:Q.171, D:M.173, D:T.174, D:T.174, D:T.174, D:G.179, D:S.180, D:S.180, D:E.429, D:T.431, D:T.431, D:N.433, D:V.434, C:E.402, C:G.406 Water bridges: D:T.174, D:G.178, D:F.210, D:S.212, D:S.212, C:R.324, C:H.334, C:H.334, C:H.337, C:H.337, C:E.402, C:E.402, C:A.407, C:A.407 Salt bridges: C:R.324, C:R.324 pi-Stacking: C:H.334, C:H.334

2 x MFK: decanoyl-CoA(Non-covalent)

MFK.2: 25 residues within 4Å: Chain B: S.129, C.130, A.133, M.173, T.174, G.179, S.180, S.232, R.233, V.288, K.289, A.292, L.295, N.296, R.299, N.302, R.379, F.425, W.428, E.429, G.430, V.434, D.438, R.441 Ligands: FAD.3 19 PLIP interactions: 19 interactions with chain B Hydrophobic interactions: B:F.425, B:W.428, B:W.428, B:E.429 Hydrogen bonds: B:G.179, B:S.180, B:S.232, B:S.232, B:R.233, B:N.296, B:N.296, B:R.299, B:R.299, B:E.429, B:R.441 Water bridges: B:V.182, B:R.379, B:R.441 pi-Cation interactions: B:R.379 MFK.5: 25 residues within 4Å: Chain D: S.129, C.130, A.133, M.173, T.174, G.179, S.180, S.232, R.233, V.288, K.289, A.292, L.295, N.296, R.299, N.302, R.379, F.425, W.428, E.429, G.430, V.434, D.438, R.441 Ligands: FAD.6 20 PLIP interactions: 20 interactions with chain D Hydrophobic interactions: D:F.425, D:W.428, D:W.428, D:E.429 Hydrogen bonds: D:G.179, D:S.180, D:S.232, D:S.232, D:R.233, D:N.296, D:N.296, D:R.299, D:R.299, D:E.429, D:E.429, D:R.441 Water bridges: D:V.182, D:R.379, D:R.441 pi-Cation interactions: D:R.379

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lepore, R. et al., Target highlights in CASP13: Experimental target structures through the eyes of their authors. Proteins (2019)

Release Date

2019-09-11

Peptides

Probable acyl-CoA dehydrogenase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Probable acyl-CoA dehydrogenase

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