SMTL ID : 6cmz.2 (1 other biounit)

2.3 Angstrom Resolution Crystal Structure of Dihydrolipoamide Dehydrogenase from Burkholderia cenocepacia in Complex with FAD and NAD

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-dimer

Ligands

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.1: 2 residues within 4Å: Chain A: R.458, H.462 Ligand excluded by PLIP

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

FAD.2: 42 residues within 4Å: Chain A: I.14, G.15, G.16, G.17, P.18, G.19, V.37, E.38, R.39, D.40, R.41, G.44, T.45, C.46, I.49, G.50, C.51, S.54, K.55, G.119, E.120, A.121, A.148, T.149, G.150, S.151, S.168, L.172, Y.188, I.189, R.274, R.277, F.281, G.312, D.313, M.319, L.320, A.321, H.322, A.324 Chain B: H.445, P.446 30 PLIP interactions: 29 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:L.172, A:I.189 Hydrogen bonds: A:G.16, A:G.19, A:G.20, A:R.39, A:R.39, A:D.40, A:T.45, A:T.45, A:C.46, A:S.54, A:K.55, A:A.121, A:A.121, A:S.151, A:Y.188, A:R.277, A:D.313, A:M.319, A:A.321, A:H.322, B:H.445 Water bridges: A:G.17, A:G.17, A:V.314, A:V.314, A:A.324 pi-Stacking: A:Y.188 pi-Cation interactions: A:R.39 FAD.5: 39 residues within 4Å: Chain A: H.445, P.446 Chain B: I.14, G.15, G.16, G.17, P.18, G.19, V.37, E.38, R.39, R.41, G.44, T.45, C.46, G.50, C.51, S.54, K.55, G.119, E.120, A.121, A.148, T.149, G.150, S.151, S.168, L.172, Y.188, I.189, R.274, R.277, F.281, G.312, D.313, M.319, L.320, A.321, H.322 29 PLIP interactions: 28 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:L.172, B:I.189, B:I.189 Hydrogen bonds: B:G.16, B:G.19, B:R.39, B:T.45, B:T.45, B:T.45, B:C.46, B:K.55, B:A.121, B:A.121, B:S.151, B:Y.188, B:R.277, B:D.313, B:M.319, B:A.321, A:H.445 Water bridges: B:G.17, B:G.20, B:E.38, B:R.41, B:G.150, B:G.150 pi-Stacking: B:Y.188 pi-Cation interactions: B:R.39, B:R.39

2 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.3: 15 residues within 4Å: Chain A: L.156, V.184, G.185, G.187, V.207, E.208, A.209, P.215, H.240, K.241, V.242, A.271, V.272, G.273, E.317 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:A.209, A:V.242, A:V.242 Water bridges: A:E.208, A:G.273, A:R.274 ADP.6: 11 residues within 4Å: Chain B: L.156, V.184, G.185, G.187, E.208, A.209, P.215, V.242, A.271, V.272, G.273 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:A.186, B:G.187, B:A.209, B:V.242, B:V.242 Water bridges: B:R.274

1 x MLT: D-MALATE(Non-covalent)

MLT.4: 8 residues within 4Å: Chain A: R.386, L.390, G.417, L.448 Chain B: E.356, G.417, S.419, E.420 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:S.419, B:E.420 Water bridges: B:E.420 Salt bridges: A:R.386

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Minasov, G. et al., 2.3 Angstrom Resolution Crystal Structure of Dihydrolipoamide Dehydrogenase from Burkholderia cenocepacia in Complex with FAD and NAD. To Be Published

Release Date

2018-03-21

Peptides

Dihydrolipoyl dehydrogenase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

Dihydrolipoyl dehydrogenase

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