SMTL ID : 1v59.1

Crystal structure of yeast lipoamide dehydrogenase complexed with NAD+

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-dimer

Ligands

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

PO4.1: 5 residues within 4Å: Chain A: I.2, V.138, K.139, E.140, H.142 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.139, A:E.140 Salt bridges: A:K.139, A:H.142

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

FAD.2: 39 residues within 4Å: Chain A: I.11, G.12, G.13, G.14, P.15, A.16, V.34, E.35, K.36, R.37, G.42, T.43, C.44, V.47, G.48, C.49, S.52, K.53, G.116, N.117, G.118, A.152, T.153, G.154, S.155, S.173, I.194, R.285, Y.288, G.324, D.325, M.331, L.332, A.333, H.334, A.336, Y.364 Chain B: H.457, P.458 33 PLIP interactions: 31 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:T.43, A:I.194, A:I.194 Hydrogen bonds: A:G.13, A:A.16, A:K.36, A:R.37, A:R.37, A:T.43, A:T.43, A:T.43, A:C.44, A:S.52, A:K.53, A:G.118, A:G.118, A:S.155, A:D.325, A:M.331, A:A.333, A:H.334, A:H.334, B:H.457 Water bridges: A:G.13, A:G.14, A:G.42, A:G.154, A:S.155, A:Y.288, A:V.326, A:Y.364, B:H.457 pi-Cation interactions: A:K.36 FAD.4: 39 residues within 4Å: Chain A: H.457, P.458 Chain B: I.11, G.12, G.13, G.14, P.15, A.16, V.34, E.35, K.36, R.37, G.42, T.43, C.44, V.47, G.48, C.49, S.52, K.53, G.116, N.117, G.118, A.152, T.153, G.154, S.155, S.173, I.194, R.285, Y.288, G.324, D.325, M.331, L.332, A.333, H.334, A.336, Y.364 33 PLIP interactions: 30 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:T.43, B:I.194, B:I.194 Hydrogen bonds: B:G.13, B:G.14, B:A.16, B:G.17, B:K.36, B:R.37, B:T.43, B:T.43, B:C.44, B:K.53, B:N.117, B:G.118, B:G.118, B:S.155, B:D.325, B:M.331, B:A.333, B:H.334, B:H.334, A:H.457 Water bridges: B:K.36, B:K.36, B:G.42, B:G.154, B:S.155, B:Y.288, B:V.326, A:H.457, A:H.457 pi-Cation interactions: B:K.36

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

NAD.3: 16 residues within 4Å: Chain A: F.160, I.189, G.190, G.191, G.192, V.212, E.213, F.214, Q.215, A.220, T.245, K.246, V.247, A.282, V.283, G.284 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:G.191, A:F.214, A:V.247 Water bridges: A:A.220, A:R.285 NAD.5: 15 residues within 4Å: Chain B: F.160, I.189, G.190, G.191, G.192, V.212, E.213, F.214, Q.215, T.245, K.246, V.247, A.282, V.283, G.284 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:G.191, B:F.214, B:V.247, B:V.247 Water bridges: B:I.193, B:I.194, B:G.284

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Adachi, W. et al., Crystal structure of yeast lipoamide dehydrogenase complexed with NAD+. To be Published

Release Date

2005-02-15

Peptides

Dihydrolipoamide dehydrogenase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Dihydrolipoamide dehydrogenase

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