SMTL ID : 1ukw.2 (1 other biounit)

Crystal structure of medium-chain acyl-CoA dehydrogenase from Thermus thermophilus HB8

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-tetramer

Ligands

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

FAD.1: 32 residues within 4Å: Chain A: F.122, L.124, S.125, N.129, G.130, S.131, W.155, I.156, S.157, K.200, T.208, L.357, I.360, Y.361, E.362, G.363, T.364, E.366, L.370 Chain B: Q.278 Chain C: R.267, A.269, F.270, I.274, F.277, I.280, Q.335, I.336, H.337, G.338, G.339, Y.340 27 PLIP interactions: 21 interactions with chain A, 5 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: A:W.155, A:K.200, A:T.208, A:L.357, A:L.357, A:Y.361 Hydrogen bonds: A:F.122, A:L.124, A:S.125, A:S.125, A:S.131, A:S.157, A:E.362, A:G.363, A:T.364, A:T.364, A:E.366, C:Q.335, C:G.339, B:Q.278 Water bridges: A:G.130, A:D.132, A:W.155, C:R.267 pi-Stacking: A:Y.361 Salt bridges: C:R.267, C:R.267 FAD.3: 31 residues within 4Å: Chain A: Q.278 Chain B: F.122, L.124, S.125, N.129, G.130, S.131, W.155, I.156, S.157, K.200, T.208, L.357, I.360, Y.361, E.362, G.363, T.364, E.366, L.370 Chain D: R.267, A.269, F.270, I.274, F.277, I.280, Q.335, I.336, G.338, G.339, Y.340 26 PLIP interactions: 19 interactions with chain B, 6 interactions with chain D, 1 interactions with chain A Hydrophobic interactions: B:W.155, B:K.200, B:L.357, B:L.357, B:Y.361 Hydrogen bonds: B:F.122, B:L.124, B:S.125, B:S.125, B:S.131, B:S.157, B:E.362, B:G.363, B:T.364, B:T.364, B:E.366, D:Q.335, D:G.339, A:Q.278 Water bridges: B:G.130, B:S.131, D:R.267, D:R.267 pi-Stacking: B:Y.361 Salt bridges: D:R.267, D:R.267 FAD.4: 32 residues within 4Å: Chain A: R.267, A.269, F.270, I.274, F.277, I.280, Q.335, I.336, H.337, G.338, G.339, Y.340 Chain C: F.122, L.124, S.125, N.129, G.130, S.131, W.155, I.156, S.157, K.200, T.208, L.357, I.360, Y.361, E.362, G.363, T.364, E.366, L.370 Chain D: Q.278 25 PLIP interactions: 19 interactions with chain C, 1 interactions with chain D, 5 interactions with chain A Hydrophobic interactions: C:W.155, C:K.200, C:T.208, C:L.357, C:L.357, C:Y.361 Hydrogen bonds: C:F.122, C:L.124, C:S.125, C:S.125, C:S.131, C:S.157, C:E.362, C:G.363, C:T.364, D:Q.278, A:Q.335, A:G.339 Water bridges: C:G.130, C:D.132, C:W.155, A:R.267 pi-Stacking: C:Y.361 Salt bridges: A:R.267, A:R.267 FAD.6: 31 residues within 4Å: Chain B: R.267, A.269, F.270, I.274, F.277, I.280, Q.335, I.336, G.338, G.339, Y.340 Chain C: Q.278 Chain D: F.122, L.124, S.125, N.129, G.130, S.131, W.155, I.156, S.157, K.200, T.208, L.357, I.360, Y.361, E.362, G.363, T.364, E.366, L.370 24 PLIP interactions: 6 interactions with chain B, 17 interactions with chain D, 1 interactions with chain C Hydrogen bonds: B:Q.335, B:G.339, D:F.122, D:L.124, D:S.125, D:S.125, D:S.131, D:S.157, D:E.362, D:G.363, D:T.364, C:Q.278 Water bridges: B:R.267, B:R.267, D:G.130, D:S.131 Salt bridges: B:R.267, B:R.267 Hydrophobic interactions: D:W.155, D:K.200, D:L.357, D:L.357, D:Y.361 pi-Stacking: D:Y.361

2 x CO: COBALT (II) ION(Non-covalent)

CO.2: 2 residues within 4Å: Chain B: D.145, H.146 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.145, B:D.145, B:H.146, H2O.8 CO.5: 2 residues within 4Å: Chain D: D.145, H.146 4 PLIP interactions: 3 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.145, D:D.145, D:H.146, H2O.16

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hamada, K. et al., Crystal structure of Thermus thermophilus medium-chain acyl-CoA dehydrogenase. To be published

Release Date

2004-11-09

Peptides

acyl-CoA dehydrogenase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

acyl-CoA dehydrogenase

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