SMTL ID : 6cmz.1 (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: G.439 Chain B: R.26 Ligand excluded by PLIP

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

FAD.2: 39 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, G.50, C.51, S.54, K.55, G.119, E.120, A.121, A.148, T.149, G.150, S.151, S.168, Y.188, I.189, R.274, R.277, F.281, G.312, D.313, M.319, L.320, A.321, H.322 Chain B: H.445, P.446 30 PLIP interactions: 29 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:I.189, A:I.189 Hydrogen bonds: A:G.16, A:G.19, A:R.39, 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:R.41, A:G.44, A:S.151, A:R.277, A:V.314, A:V.314 pi-Stacking: A:Y.188 pi-Cation interactions: A:R.39 FAD.3: 17 residues within 4Å: Chain A: V.154, 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, R.293, E.317 Ligands: FMN.5 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:A.209, A:V.242, A:V.242, A:R.293, A:E.317 Water bridges: A:I.189 FAD.6: 40 residues within 4Å: Chain A: H.445, P.446 Chain B: I.14, G.15, G.16, G.17, P.18, G.19, E.38, R.39, D.40, 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, A.324 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:D.40, B:T.45, B:T.45, B:T.45, B:C.46, B:S.54, 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:R.41, B:G.44, B:G.150 pi-Stacking: B:Y.188 pi-Cation interactions: B:R.39

1 x NAD: NICOTINAMIDE-ADENINE-DINUCLEOTIDE(Non-covalent)

NAD.4: 4 residues within 4Å: Chain A: L.236, W.237, H.240, Q.261 1 PLIP interactions: 1 interactions with chain A pi-Stacking: A:W.237

1 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.5: 5 residues within 4Å: Chain A: L.156, P.157, S.158, R.293 Ligands: FAD.3 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:P.157

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

ADP.7: 12 residues within 4Å: Chain B: V.154, L.156, P.157, G.185, A.186, G.187, E.208, A.209, P.215, A.271, V.272, G.273 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:G.187, B:A.209 Water bridges: B:Y.188, B:E.317

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
A

B
B

Dihydrolipoyl dehydrogenase

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