SMTL ID : 6lq6.1

Crystal Structure of E447A Acyl-CoA Dehydrogenase FadE5 mutant from Mycobacteria smegmatis in complex with C20CoA

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 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: DCR.2, COA.3 35 PLIP interactions: 24 interactions with chain A, 11 interactions with chain B Hydrophobic interactions: A:F.197, A:K.259, A:T.267, 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:T.166, A:G.171, A:R.196, A:T.450, A:A.452, A:Q.456, A:Q.456, B:Y.323, B:R.327, B:Q.329, B:D.351, B:Q.421, B:S.426 Salt bridges: B:R.327, B:R.327 pi-Stacking: B:H.349 FAD.4: 27 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 Ligands: DCR.5, COA.6 34 PLIP interactions: 21 interactions with chain B, 13 interactions with chain A Hydrophobic interactions: B:F.197, B:K.259, B:T.267, 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:T.450, B:A.452, B:Q.456, B:Q.456, B:Q.456, A:Y.323, A:Y.323, A:R.327, A:R.327, A:Q.329, A:A.331, A:A.331 Salt bridges: A:R.327, A:R.327 pi-Stacking: A:H.349

2 x DCR: icosanoic acid(Non-covalent)

DCR.2: 16 residues within 4Å: Chain A: G.97, L.98, M.128, M.131, G.134, M.135, E.137, A.161, T.199, V.297, Q.300, M.304, Y.447, A.448 Ligands: FAD.1, COA.3 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:L.98, A:M.131, A:M.135, A:E.137, A:A.161, A:V.297, A:Q.300, A:Q.300 Hydrogen bonds: A:A.448 DCR.5: 19 residues within 4Å: Chain B: R.109, Q.112, I.116, Y.127, M.131, G.134, M.135, I.138, A.161, T.162, M.163, T.199, V.297, Q.300, M.304, Y.447, A.448 Ligands: FAD.4, COA.6 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:I.116, B:M.131, B:M.135, B:I.138, B:T.199, B:V.297, B:Q.300, B:Y.447, B:Y.447 Hydrogen bonds: B:A.448

2 x COA: COENZYME A(Non-covalent)

COA.3: 22 residues within 4Å: Chain A: M.163, L.165, 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, DCR.2 24 PLIP interactions: 22 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:F.295 Hydrogen bonds: A:S.172, A:T.225, A:R.302, A:R.461, A:K.462, A:K.462 Water bridges: A:G.171, A:K.226, A:K.226, A:R.302, A:R.302, A:R.302, A:Q.456, A:R.461, B:K.339 Salt bridges: A:K.226, A:R.461, A:R.465, B:K.339 pi-Stacking: A:F.295, A:F.295 pi-Cation interactions: A:R.461, A:R.461 COA.6: 22 residues within 4Å: Chain A: K.339 Chain B: M.163, L.165, T.166, S.172, V.174, T.225, K.226, I.291, A.292, F.295, E.299, R.302, A.448, G.449, I.453, D.457, R.461, K.462, R.465 Ligands: FAD.4, DCR.5 28 PLIP interactions: 26 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:F.295 Hydrogen bonds: B:S.172, B:E.299, B:R.302, B:K.462, B:K.462 Water bridges: B:G.171, B:T.225, B:K.226, B:K.226, B:A.292, B:R.302, B:R.302, B:R.302, B:Q.456, B:D.457, B:R.461, B:R.465, B:R.465 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. 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

2020-07-01

Peptides

Acyl-CoA dehydrogenase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Acyl-CoA dehydrogenase

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