SMTL ID : 8pns.1

Crystal structure of the acyl-CoA dehydrogenase PA0506 (FadE1) from Pseudomonas aeruginosa

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.08 Å

Oligo State

homo-dimer

Ligands

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

FAD.1: 28 residues within 4Å: Chain A: M.165, L.167, T.168, G.173, T.174, F.199, I.200, S.201, I.262, I.438, L.441, Y.442, E.443, T.445, L.451 Chain B: R.323, Q.325, M.326, I.342, H.345, M.351, Q.416, I.417, F.418, G.419, G.420, H.421 Ligands: CO8.3 31 PLIP interactions: 19 interactions with chain A, 12 interactions with chain B Hydrophobic interactions: A:F.199, A:I.262, A:I.438 Hydrogen bonds: A:M.165, A:L.167, A:T.168, A:T.168, A:T.174, A:T.174, A:S.201, A:E.443, A:T.445, B:Q.325, B:Q.416, B:G.420, B:H.421 Water bridges: A:M.165, A:T.168, A:G.173, A:G.447, A:G.447, A:G.447, B:R.323, B:H.345, B:Q.416, B:H.421 pi-Stacking: A:Y.442, B:H.345 Salt bridges: B:R.323, B:R.323, B:H.421 FAD.5: 30 residues within 4Å: Chain A: R.323, Q.325, M.326, I.342, H.345, V.348, M.351, Q.416, I.417, F.418, G.419, G.420, H.421 Chain B: M.165, L.167, T.168, G.173, T.174, F.199, I.200, S.201, K.259, I.262, T.267, I.438, L.441, Y.442, T.445, L.451 Ligands: CO8.6 34 PLIP interactions: 15 interactions with chain A, 19 interactions with chain B Hydrogen bonds: A:Q.325, A:Q.416, A:G.420, A:H.421, B:M.165, B:L.167, B:T.168, B:T.168, B:T.174, B:S.201, B:E.443, B:T.445, B:T.445 Water bridges: A:R.323, A:H.345, A:H.345, A:Q.416, A:H.421, A:H.421, A:H.421, B:T.168, B:G.173, B:G.447 Salt bridges: A:R.323, A:R.323, A:H.421 pi-Stacking: A:H.345, B:Y.442 Hydrophobic interactions: B:F.199, B:K.259, B:I.262, B:T.267, B:I.438, B:I.438

2 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.2: 8 residues within 4Å: Chain A: N.295, T.296, L.299, L.392, A.393, T.396, K.457 Ligands: CO8.3 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.295, A:L.299, A:T.396, A:K.457, A:K.457 PEG.4: 8 residues within 4Å: Chain A: K.259, M.260, H.263, E.430, R.434 Chain B: K.259, M.260, H.263 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Water bridges: B:R.434 Hydrogen bonds: A:K.259, A:E.430

2 x CO8: OCTANOYL-COENZYME A(Non-covalent)

CO8.3: 23 residues within 4Å: Chain A: L.132, M.165, L.167, G.173, T.174, L.176, T.226, L.287, N.288, F.291, M.294, N.295, R.298, T.301, Y.442, E.443, G.444, V.448, D.452, R.456, K.457 Ligands: FAD.1, PEG.2 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:L.132, A:L.287, A:F.291, A:Y.442, A:Y.442, A:E.443 Hydrogen bonds: A:N.295, A:R.298, A:E.443, A:D.452, A:K.457 Water bridges: A:G.173 Salt bridges: A:R.456, A:R.456 pi-Stacking: A:F.291, A:F.291 pi-Cation interactions: A:R.456 CO8.6: 23 residues within 4Å: Chain A: M.326 Chain B: M.128, M.165, L.167, G.173, T.174, L.176, T.226, L.287, N.288, F.291, M.294, N.295, R.298, T.301, Y.442, E.443, G.444, V.448, D.452, R.456, K.457 Ligands: FAD.5 19 PLIP interactions: 19 interactions with chain B Hydrophobic interactions: B:L.176, B:F.291, B:Y.442, B:Y.442, B:Y.442, B:V.448 Hydrogen bonds: B:T.226, B:N.288, B:N.295, B:R.298, B:E.443, B:D.452, B:K.457 Water bridges: B:G.173 Salt bridges: B:R.456, B:R.456 pi-Stacking: B:F.291, B:F.291 pi-Cation interactions: B:R.456

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, M. et al., Characterization of two acyl-CoA dehydrogenases from P. aeruginosa. To Be Published

Release Date

2025-01-15

Peptides

Acyl-CoA dehydrogenase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Acyl-CoA dehydrogenase