SMTL ID : 2yqu.1

Crystal structures and evolutionary relationship of two different lipoamide dehydrogenase(E3s) from Thermus thermophilus

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-dimer

Ligands

3 x CO3: CARBONATE ION(Non-functional Binders)

CO3.1: 8 residues within 4Å: Chain A: P.11, Y.14, A.310, H.311, S.314 Chain B: H.434, E.439, H.454 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Water bridges: B:E.439, A:S.314, A:S.314 CO3.3: 2 residues within 4Å: Chain B: S.423, D.426 2 PLIP interactions: 2 interactions with chain B Water bridges: B:S.423, B:E.425 CO3.4: 7 residues within 4Å: Chain A: H.434, E.439, H.454 Chain B: P.11, A.310, H.311, S.314 9 PLIP interactions: 5 interactions with chain A, 4 interactions with chain B Water bridges: A:H.434, A:E.439, A:K.442, A:K.442, A:H.454, B:Y.14, B:S.314, B:S.314 Hydrogen bonds: B:S.314

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

FAD.2: 41 residues within 4Å: Chain A: I.7, G.8, G.10, P.11, G.12, G.13, V.30, E.31, K.32, E.33, G.38, T.39, C.40, R.42, V.43, G.44, C.45, S.48, K.49, G.109, T.110, A.111, A.136, T.137, G.138, S.139, S.157, I.178, R.262, Y.265, L.269, G.301, D.302, M.308, L.309, A.310, H.311, A.313, Y.341 Chain B: H.434, P.435 30 PLIP interactions: 27 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:T.39, A:I.178, A:I.178, A:I.178 Hydrogen bonds: A:G.10, A:G.12, A:G.13, A:K.32, A:T.39, A:T.39, A:T.39, A:C.40, A:R.42, A:S.48, A:K.49, A:A.111, A:A.111, A:S.139, A:D.302, A:M.308, A:A.310, B:H.434 Water bridges: A:G.38, A:G.138, A:D.302, A:D.302, A:V.303, B:H.434, B:H.434 pi-Cation interactions: A:K.32 FAD.6: 40 residues within 4Å: Chain A: H.434, P.435 Chain B: I.7, G.8, G.10, P.11, G.12, V.30, E.31, K.32, E.33, G.38, T.39, C.40, R.42, V.43, G.44, C.45, S.48, K.49, G.109, T.110, A.111, A.136, T.137, G.138, S.139, S.157, I.178, R.262, Y.265, L.269, G.301, D.302, M.308, L.309, A.310, H.311, A.313, Y.341 31 PLIP interactions: 29 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:T.39, B:I.178, B:I.178, B:I.178 Hydrogen bonds: B:G.10, B:G.12, B:G.13, B:K.32, B:T.39, B:T.39, B:C.40, B:R.42, B:S.48, B:K.49, B:A.111, B:A.111, B:S.139, B:D.302, B:M.308, B:A.310, A:H.434 Water bridges: B:K.32, B:K.32, B:G.38, B:T.39, B:T.39, B:G.138, B:V.303, B:Y.341, A:H.434 pi-Cation interactions: B:K.32

1 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.5: 2 residues within 4Å: Chain B: R.396, K.421 3 PLIP interactions: 3 interactions with chain B Water bridges: B:R.396 Salt bridges: B:R.396, B:K.421

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kondo, H. et al., Crystal structures and evolutionary relationship of two different lipoamide dehydrogenase(E3s) from Thermus thermophilus. To be Published

Release Date

2008-04-01

Peptides

2-oxoglutarate dehydrogenase E3 component: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

2-oxoglutarate dehydrogenase E3 component

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