SMTL ID : 1x7y.1

Crystal structure of the human mitochondrial branched-chain alpha-ketoacid dehydrogenase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.57 Å

Oligo State

hetero-2-2-mer

Ligands

4 x K: POTASSIUM ION(Non-covalent)

K.1: 5 residues within 4Å: Chain A: Q.112, S.161, P.163, T.166, Q.167 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:S.161, A:S.161, A:P.163, H2O.1 K.5: 7 residues within 4Å: Chain B: G.128, L.130, T.131, C.178, I.179, D.181, N.183 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:L.130, B:C.178, B:D.181, B:N.183, H2O.17 K.7: 5 residues within 4Å: Chain C: Q.112, S.161, P.163, T.166, Q.167 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:S.161, C:S.161, C:P.163, H2O.28 K.11: 7 residues within 4Å: Chain D: G.128, L.130, T.131, C.178, I.179, D.181, N.183 5 PLIP interactions: 4 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:L.130, D:C.178, D:D.181, D:N.183, H2O.45

2 x MN: MANGANESE (II) ION(Non-covalent)

MN.2: 4 residues within 4Å: Chain A: E.193, N.222, Y.224 Ligands: TPP.4 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.193, A:E.193, A:Y.224, H2O.1 MN.8: 4 residues within 4Å: Chain C: E.193, N.222, Y.224 Ligands: TPP.10 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:E.193, C:E.193, C:Y.224, H2O.29

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.3: 4 residues within 4Å: Chain A: Y.113 Chain D: Y.102, H.146 Ligands: TPP.4 Ligand excluded by PLIP CL.9: 4 residues within 4Å: Chain B: Y.102, H.146 Chain C: Y.113 Ligands: TPP.10 Ligand excluded by PLIP

2 x TPP: THIAMINE DIPHOSPHATE(Non-covalent)

TPP.4: 21 residues within 4Å: Chain A: R.114, S.162, P.163, L.164, G.192, E.193, G.194, A.195, E.198, R.220, N.222, Y.224, A.225, I.226 Chain D: E.46, L.74, E.76, Q.98, Y.102 Ligands: MN.2, CL.3 19 PLIP interactions: 2 interactions with chain D, 17 interactions with chain A Hydrophobic interactions: D:Y.102, A:A.225, A:I.226, A:I.226 pi-Stacking: D:Y.102 Hydrogen bonds: A:S.162, A:G.192, A:E.193, A:G.194, A:A.195 Water bridges: A:R.114, A:R.114, A:R.220, A:R.220, A:R.220, A:R.220, A:I.226 Salt bridges: A:R.114, A:R.220 TPP.10: 21 residues within 4Å: Chain B: E.46, L.74, E.76, Q.98, Y.102 Chain C: R.114, S.162, P.163, L.164, G.192, E.193, G.194, A.195, E.198, R.220, N.222, Y.224, A.225, I.226 Ligands: MN.8, CL.9 21 PLIP interactions: 2 interactions with chain B, 19 interactions with chain C Hydrophobic interactions: B:Y.102, C:A.225, C:I.226, C:I.226 pi-Stacking: B:Y.102 Hydrogen bonds: C:S.162, C:G.192, C:E.193, C:G.194, C:A.195, C:E.198, C:N.222 Water bridges: C:R.114, C:R.114, C:R.220, C:R.220, C:R.220, C:R.220, C:I.226 Salt bridges: C:R.114, C:R.220

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 8 residues within 4Å: Chain A: Q.374 Chain B: W.260, E.290, T.294, E.297 Chain D: L.283, T.284, R.309 8 PLIP interactions: 3 interactions with chain D, 1 interactions with chain A, 4 interactions with chain B Hydrogen bonds: D:T.284, D:R.309, B:E.290, B:E.297 Water bridges: D:T.284, A:Q.378, B:W.260, B:E.297 GOL.12: 8 residues within 4Å: Chain B: L.283, T.284, R.309 Chain C: Q.374 Chain D: W.260, E.290, T.294, E.297 8 PLIP interactions: 1 interactions with chain C, 4 interactions with chain B, 3 interactions with chain D Water bridges: C:Q.378, B:T.284, D:W.260 Hydrogen bonds: B:T.284, B:T.284, B:R.309, D:T.294, D:E.297

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wynn, R.M. et al., Molecular mechanism for regulation of the human mitochondrial branched-chain alpha-ketoacid dehydrogenase complex by phosphorylation. Structure (2004)

Release Date

2004-11-23

Peptides

2-oxoisovalerate dehydrogenase alpha subunit: AC
2-oxoisovalerate dehydrogenase beta subunit: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
A

B
B

D
B

2-oxoisovalerate dehydrogenase alpha subunit

2-oxoisovalerate dehydrogenase beta subunit

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