SMTL ID : 2bfb.1

Reactivity modulation of human branched-chain alpha-ketoacid dehydrogenase by an internal molecular switch

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.77 Å

Oligo State

hetero-2-2-mer

Ligands

4 x K: POTASSIUM ION(Non-covalent)

K.1: 4 residues within 4Å: Chain A: S.161, P.163, T.166, Q.167 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:S.161, A:S.161, A:P.163, H2O.6, H2O.8 K.6: 8 residues within 4Å: Chain B: G.128, L.130, T.131, C.178, I.179, D.181, N.183, C.185 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.20 K.9: 4 residues within 4Å: Chain C: S.161, P.163, T.166, Q.167 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:S.161, C:S.161, C:P.163, H2O.30, H2O.33 K.14: 8 residues within 4Å: Chain D: G.128, L.130, T.131, C.178, I.179, D.181, N.183, C.185 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.44

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.14 MN.10: 4 residues within 4Å: Chain C: E.193, N.222, Y.224 Ligands: TPP.12 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:E.193, C:E.193, C:Y.224, H2O.39

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

CL.3: 6 residues within 4Å: Chain A: A.112, L.164, A.165, Q.167, F.191, A.195 Ligand excluded by PLIP CL.5: 1 residues within 4Å: Chain A: Y.113 Ligand excluded by PLIP CL.11: 6 residues within 4Å: Chain C: A.112, L.164, A.165, Q.167, F.191, A.195 Ligand excluded by PLIP CL.13: 1 residues within 4Å: Chain C: Y.113 Ligand excluded by PLIP

2 x TPP: THIAMINE DIPHOSPHATE(Non-covalent)

TPP.4: 21 residues within 4Å: Chain A: Y.113, 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 26 PLIP interactions: 23 interactions with chain A, 3 interactions with chain D Hydrophobic interactions: A:L.164, A:A.225, A:I.226, A:I.226, D:Y.102 Hydrogen bonds: A:Y.113, A:Y.113, A:S.162, A:G.192, A:E.193, A:G.194, A:A.195 Water bridges: A:R.114, A:R.220, A:R.220, A:R.220, A:R.220, A:R.220, A:N.222, A:N.222, A:N.222, A:R.287, D:Y.102 Salt bridges: A:R.114, A:R.220 pi-Stacking: D:Y.102 TPP.12: 21 residues within 4Å: Chain B: E.46, L.74, E.76, Q.98, Y.102 Chain C: Y.113, 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.10 25 PLIP interactions: 23 interactions with chain C, 2 interactions with chain B Hydrophobic interactions: C:L.164, C:A.225, C:I.226, C:I.226, B:Y.102 Hydrogen bonds: C:Y.113, 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.220, C:R.220, C:R.220, C:R.220, C:R.220, C:N.222, C:N.222, C:R.287 Salt bridges: C:R.114, C:R.220 pi-Stacking: B:Y.102

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 7 residues within 4Å: Chain A: Q.374 Chain B: W.260, E.290, T.294 Chain D: L.283, T.284, R.309 8 PLIP interactions: 5 interactions with chain B, 3 interactions with chain D Hydrogen bonds: B:E.290, B:E.290, B:E.297, D:R.309 Water bridges: B:W.260, B:E.297, D:T.284, D:D.314 GOL.15: 7 residues within 4Å: Chain B: L.283, T.284, R.309 Chain C: Q.374 Chain D: W.260, E.290, T.294 8 PLIP interactions: 4 interactions with chain D, 4 interactions with chain B Hydrogen bonds: D:E.290, D:T.294, D:E.297, B:T.284, B:R.309 Water bridges: D:W.260, B:T.284, B:D.314

2 x MRD: (4R)-2-METHYLPENTANE-2,4-DIOL(Non-functional Binders)

MRD.8: 1 residues within 4Å: Chain B: V.58 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:V.58 MRD.16: 1 residues within 4Å: Chain D: V.58 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:V.58

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Machius, M. et al., A Versatile Conformational Switch Regulates Reactivity in Human Branched-Chain Alpha-Ketoacid Dehydrogenase. Structure (2006)

Release Date

2006-02-16

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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