SMTL ID : 4e01.2 (1 other biounit)

Crystal structure of branched-chain alpha-ketoacid dehydrogenase kinase/3,6-dichlorobenzo[b]thiophene-2-carboxylic acid complex with AMPPNP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.97 Å

Oligo State

homo-tetramer

Ligands

4 x 0F1: 3,6-dichloro-1-benzothiophene-2-carboxylic acid(Non-covalent)

0F1.1: 10 residues within 4Å: Chain A: L.98, I.102, Y.129, V.155, L.158, L.159, H.162, R.197, I.200, R.201 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:I.102, A:L.158, A:L.158, A:I.200 Hydrogen bonds: A:Y.129 Salt bridges: A:H.162, A:R.197, A:R.201 0F1.5: 10 residues within 4Å: Chain B: L.98, I.102, Y.129, V.155, L.158, L.159, H.162, R.197, I.200, R.201 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:I.102, B:L.158, B:L.158, B:I.200 Hydrogen bonds: B:Y.129 Salt bridges: B:H.162, B:R.197, B:R.201 0F1.9: 10 residues within 4Å: Chain C: L.98, I.102, Y.129, V.155, L.158, L.159, H.162, R.197, I.200, R.201 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:I.102, C:L.158, C:L.158, C:I.200 Salt bridges: C:H.162, C:R.197, C:R.201 0F1.13: 10 residues within 4Å: Chain D: L.98, I.102, Y.129, V.155, L.158, L.159, H.162, R.197, I.200, R.201 7 PLIP interactions: 7 interactions with chain D Hydrophobic interactions: D:I.102, D:L.158, D:L.158, D:I.200 Salt bridges: D:H.162, D:R.197, D:R.201

4 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 2 residues within 4Å: Chain A: N.279 Ligands: ANP.4 No protein-ligand interaction detected (PLIP) MG.6: 2 residues within 4Å: Chain B: N.279 Ligands: ANP.8 No protein-ligand interaction detected (PLIP) MG.10: 2 residues within 4Å: Chain C: N.279 Ligands: ANP.12 No protein-ligand interaction detected (PLIP) MG.14: 2 residues within 4Å: Chain D: N.279 Ligands: ANP.16 No protein-ligand interaction detected (PLIP)

4 x K: POTASSIUM ION(Non-covalent)

K.3: 6 residues within 4Å: Chain A: V.328, D.330, F.333, G.367, P.371 Ligands: ANP.4 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:V.328, A:D.330, A:F.333, A:G.367 K.7: 6 residues within 4Å: Chain B: V.328, D.330, F.333, G.367, P.371 Ligands: ANP.8 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:V.328, B:D.330, B:F.333, B:G.367 K.11: 6 residues within 4Å: Chain C: V.328, D.330, F.333, G.367, P.371 Ligands: ANP.12 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:V.328, C:D.330, C:F.333, C:G.367 K.15: 6 residues within 4Å: Chain D: V.328, D.330, F.333, G.367, P.371 Ligands: ANP.16 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:V.328, D:D.330, D:F.333, D:G.367

4 x ANP: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER(Non-covalent)

ANP.4: 22 residues within 4Å: Chain A: E.275, N.279, A.280, R.282, A.283, D.315, G.319, I.320, V.328, F.333, T.334, T.335, G.365, F.366, G.367, F.368, G.369, L.370, P.371, T.394 Ligands: MG.2, K.3 20 PLIP interactions: 20 interactions with chain A Hydrogen bonds: A:N.279, A:R.282, A:D.315, A:T.334, A:T.334, A:T.334, A:T.335, A:T.335, A:F.366, A:G.367, A:F.368, A:G.369, A:L.370 Water bridges: A:N.279, A:A.283, A:D.315, A:G.365, A:G.365, A:T.394, A:T.394 ANP.8: 22 residues within 4Å: Chain B: E.275, N.279, A.280, R.282, A.283, D.315, G.319, I.320, V.328, F.333, T.334, T.335, G.365, F.366, G.367, F.368, G.369, L.370, P.371, T.394 Ligands: MG.6, K.7 20 PLIP interactions: 20 interactions with chain B Hydrogen bonds: B:N.279, B:R.282, B:D.315, B:T.334, B:T.334, B:T.334, B:T.335, B:T.335, B:F.366, B:G.367, B:F.368, B:G.369, B:L.370 Water bridges: B:N.279, B:A.283, B:D.315, B:G.365, B:G.365, B:T.394, B:T.394 ANP.12: 22 residues within 4Å: Chain C: E.275, N.279, A.280, R.282, A.283, D.315, G.319, I.320, V.328, F.333, T.334, T.335, G.365, F.366, G.367, F.368, G.369, L.370, P.371, T.394 Ligands: MG.10, K.11 20 PLIP interactions: 20 interactions with chain C Hydrogen bonds: C:E.275, C:N.279, C:R.282, C:D.315, C:T.334, C:T.334, C:T.334, C:T.335, C:T.335, C:F.366, C:G.367, C:F.368, C:G.369, C:L.370, C:T.394 Water bridges: C:N.279, C:A.283, C:D.315, C:G.365, C:G.365 ANP.16: 22 residues within 4Å: Chain D: E.275, N.279, A.280, R.282, A.283, D.315, G.319, I.320, V.328, F.333, T.334, T.335, G.365, F.366, G.367, F.368, G.369, L.370, P.371, T.394 Ligands: MG.14, K.15 22 PLIP interactions: 22 interactions with chain D Hydrogen bonds: D:E.275, D:E.275, D:N.279, D:R.282, D:D.315, D:T.334, D:T.334, D:T.334, D:T.335, D:T.335, D:F.366, D:G.367, D:F.368, D:G.369, D:L.370, D:T.394 Water bridges: D:N.279, D:N.279, D:A.283, D:D.315, D:G.365, D:G.365

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tso, S.C. et al., Structures of branched-chain alpha-ketoacid dehydrogenase kinase-inhibitor complexes. To be Published

Release Date

2013-03-27

Peptides

[3-methyl-2-oxobutanoate dehydrogenase [lipoamide]] kinase, mitochondrial: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

[3-methyl-2-oxobutanoate dehydrogenase [lipoamide]] kinase, mitochondrial

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