SMTL ID : 6lq8.1

Crystal Structure of E447A Acyl-CoA Dehydrogenase FadE5 mutant from Mycobacteria smegmatis in complex with C22CoA

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

homo-dimer

Ligands

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

FAD.1: 28 residues within 4Å: Chain A: M.163, L.165, T.166, G.171, S.172, F.197, I.198, T.199, K.259, T.267, I.443, L.446, Y.447, A.448, T.450, A.452, I.453 Chain B: R.327, Q.329, I.346, H.349, V.352, Q.421, T.422, G.424, G.425 Ligands: EO3.2, COA.3 37 PLIP interactions: 25 interactions with chain A, 12 interactions with chain B Hydrophobic interactions: A:F.197, A:K.259, A:T.267, A:I.443, A:I.443, A:Y.447, A:Y.447 Hydrogen bonds: A:M.163, A:L.165, A:T.166, A:T.166, A:S.172, A:S.172, A:T.199, A:T.199, A:A.448, A:T.450, A:T.450, B:Q.421, B:G.425 Water bridges: A:R.196, A:T.450, A:A.452, A:Q.456, A:Q.456, A:Q.456, A:Q.456, B:Y.323, B:R.327, B:R.327, B:R.327, B:Q.329, B:Q.421, B:S.426 Salt bridges: B:R.327, B:R.327 pi-Stacking: B:H.349 FAD.4: 28 residues within 4Å: Chain A: R.327, Q.329, I.346, H.349, V.352, Q.421, T.422, G.424, G.425 Chain B: M.163, L.165, T.166, G.171, S.172, F.197, I.198, T.199, K.259, T.267, I.443, L.446, Y.447, A.448, T.450, A.452, I.453 Ligands: EO3.5, COA.6 33 PLIP interactions: 19 interactions with chain B, 14 interactions with chain A Hydrophobic interactions: B:F.197, B:K.259, B:T.267, B:I.443, B:I.443, B:Y.447, B:Y.447 Hydrogen bonds: B:M.163, B:L.165, B:T.166, B:T.166, B:S.172, B:S.172, B:T.199, B:A.448, B:T.450, A:Q.421, A:G.425, A:S.426 Water bridges: B:R.196, B:Q.456, B:Q.456, A:Y.323, A:Y.323, A:R.327, A:R.327, A:R.327, A:Q.329, A:H.349, A:Q.421 Salt bridges: A:R.327, A:R.327 pi-Stacking: A:H.349

2 x EO3: docosanoic acid(Non-covalent)

EO3.2: 23 residues within 4Å: Chain A: V.96, G.97, L.98, R.109, Q.112, M.128, M.131, G.134, M.135, E.137, I.138, A.161, M.163, T.199, S.200, V.297, Q.300, A.301, M.304, Y.447, A.448 Ligands: FAD.1, COA.3 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:L.98, A:E.137, A:I.138, A:I.138, A:T.199, A:V.297, A:Q.300, A:A.301, A:Y.447, A:Y.447, A:A.448 Hydrogen bonds: A:A.448 EO3.5: 23 residues within 4Å: Chain B: R.109, Q.112, W.113, Y.127, M.128, M.131, G.134, M.135, I.138, A.161, T.162, M.163, T.199, V.297, Q.300, A.301, M.304, V.305, Q.377, Y.447, A.448 Ligands: FAD.4, COA.6 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:R.109, B:W.113, B:M.131, B:M.135, B:I.138, B:T.199, B:Y.447, B:Y.447, B:A.448 Hydrogen bonds: B:A.448

2 x COA: COENZYME A(Non-covalent)

COA.3: 24 residues within 4Å: Chain A: M.163, L.165, T.166, G.171, S.172, V.174, T.225, K.226, I.291, A.292, F.295, I.298, E.299, R.302, A.448, G.449, I.453, D.457, R.461, K.462, R.465 Chain B: K.339 Ligands: FAD.1, EO3.2 20 PLIP interactions: 2 interactions with chain B, 18 interactions with chain A Salt bridges: B:K.339, B:K.339, A:K.226, A:R.461, A:R.465 Hydrophobic interactions: A:V.174, A:V.174, A:F.295 Hydrogen bonds: A:S.172, A:R.302, A:R.302, A:K.462, A:K.462 Water bridges: A:G.171, A:K.226, A:K.226, A:R.461 pi-Stacking: A:F.295, A:F.295 pi-Cation interactions: A:R.461 COA.6: 24 residues within 4Å: Chain A: K.339 Chain B: M.163, L.165, T.166, G.171, S.172, V.174, T.225, K.226, I.291, A.292, F.295, E.299, R.302, A.448, G.449, I.453, Q.456, D.457, R.461, K.462, R.465 Ligands: FAD.4, EO3.5 30 PLIP interactions: 26 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:F.295 Hydrogen bonds: B:S.172, B:E.299, B:R.302, B:R.302, B:K.462, B:K.462 Water bridges: B:G.171, B:T.225, B:K.226, B:K.226, B:K.226, B:Q.456, B:D.457, B:D.457, B:R.461, B:R.461, B:R.465, B:R.465, A:K.339, A:K.339 Salt bridges: B:K.226, B:R.461, B:R.465, A:K.339, A:K.339 pi-Stacking: B:F.295, B:F.295 pi-Cation interactions: B:R.461, B:R.461

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chen, X.B. et al., Structural basis for the broad substrate specificity of two acyl-CoA dehydrogenases FadE5 from mycobacteria. Proc.Natl.Acad.Sci.USA (2020)

Release Date

2020-11-25

Peptides

Acyl-CoA dehydrogenase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Acyl-CoA dehydrogenase

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