SMTL ID : 2eq7.1

Crystal structure of lipoamide dehydrogenase from thermus thermophilus HB8 with psbdo

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

hetero-oligomer

Ligands

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

FAD.1: 43 residues within 4Å: Chain A: I.7, G.8, A.9, 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 Ligands: NAD.2 29 PLIP interactions: 26 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:T.39, A:I.178 Hydrogen bonds: A:G.12, A:G.13, A:K.32, 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.10, A:G.10, A:K.32, A:E.33, A:G.38, A:G.138, A:S.139, A:V.303, B:H.434, B:H.434 pi-Cation interactions: A:K.32 FAD.3: 43 residues within 4Å: Chain A: H.434, P.435 Chain B: I.7, G.8, A.9, 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 Ligands: NAD.4 32 PLIP interactions: 29 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:T.39, B:I.178 Hydrogen bonds: 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:G.10, B:G.10, B:K.32, B:K.32, B:K.32, B:E.33, B:G.38, B:G.138, B:G.138, B:S.139, B:L.309, A:H.434, A:H.434 pi-Cation interactions: B:K.32

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

NAD.2: 22 residues within 4Å: Chain A: W.146, V.173, G.174, G.176, V.177, I.178, E.181, L.196, E.197, Y.198, M.199, P.204, V.229, V.231, A.259, V.260, G.261, R.262, M.308, L.309, V.339 Ligands: FAD.1 20 PLIP interactions: 20 interactions with chain A Hydrophobic interactions: A:V.177, A:I.178 Hydrogen bonds: A:V.177, A:I.178, A:E.181, A:Y.198, A:V.231, A:V.231, A:A.259, A:G.261 Water bridges: A:G.176, A:G.179, A:T.205, A:R.262, A:R.262, A:M.308, A:M.308, A:S.338, A:V.339, A:V.339 NAD.4: 23 residues within 4Å: Chain B: W.146, G.174, G.175, G.176, V.177, I.178, E.181, L.196, E.197, Y.198, M.199, P.204, V.229, R.230, V.231, A.259, V.260, G.261, R.262, M.308, L.309, V.339 Ligands: FAD.3 20 PLIP interactions: 20 interactions with chain B Hydrophobic interactions: B:V.177, B:V.177, B:I.178 Hydrogen bonds: B:G.175, B:V.177, B:I.178, B:E.181, B:Y.198, B:V.231, B:V.231, B:A.259, B:G.261, B:M.308 Water bridges: B:G.176, B:G.179, B:T.205, B:T.205, B:R.262, B:V.339, B:V.339

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nakai, T. et al., Crystal structure of lipoamide dehydrogenase from Thermus thermophilus HB8. To be Published

Release Date

2008-04-01

Peptides

2-oxoglutarate dehydrogenase E3 component: AB
2-oxoglutarate dehydrogenase E2 component: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

2-oxoglutarate dehydrogenase E3 component

2-oxoglutarate dehydrogenase E2 component

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