SMTL ID : 2bff.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.46 Å

Oligo State

hetero-2-2-mer

Ligands

2 x TZD: 2-{3-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-4-METHYL-2-OXO-2,3-DIHYDRO-1,3-THIAZOL-5-YL}ETHYL TRIHYDROGEN DIPHOSPHATE(Non-covalent)

TZD.1: 23 residues within 4Å: Chain A: Q.112, 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, H.291 Chain D: E.46, L.74, E.76, Q.98, Y.102 Ligands: MN.3 23 PLIP interactions: 19 interactions with chain A, 4 interactions with chain D Hydrophobic interactions: A:L.164, A:A.225, A:I.226, A:I.226, D:Y.102 Hydrogen bonds: A:Q.112, A:Q.112, A:S.162, A:G.192, A:E.193, A:G.194, A:A.195, A:H.291 Water bridges: A:R.114, A:R.114, A:R.114, A:R.220, A:N.222, D:Y.102, D:Y.102 Salt bridges: A:R.114, A:R.220 pi-Stacking: D:Y.102 TZD.6: 23 residues within 4Å: Chain B: E.46, L.74, E.76, Q.98, Y.102 Chain C: Q.112, 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, H.291 Ligands: MN.8 23 PLIP interactions: 21 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:Q.112, C:Q.112, C:S.162, C:G.192, C:E.193, C:G.194, C:A.195, C:E.198, C:N.222, C:H.291 Water bridges: C:R.114, C:R.114, C:R.114, C:R.220, C:N.222 Salt bridges: C:R.114, C:R.220 pi-Stacking: B:Y.102

4 x K: POTASSIUM ION(Non-covalent)

K.2: 4 residues within 4Å: Chain A: S.161, P.163, T.166, Q.167 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:S.161, A:S.161, A:P.163, A:T.166, H2O.6 K.4: 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.21 K.7: 4 residues within 4Å: Chain C: S.161, P.163, T.166, Q.167 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:S.161, C:S.161, C:P.163, C:T.166, H2O.32 K.9: 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.47

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

MN.3: 4 residues within 4Å: Chain A: E.193, N.222, Y.224 Ligands: TZD.1 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.193, A:E.193, A:Y.224, H2O.15 MN.8: 4 residues within 4Å: Chain C: E.193, N.222, Y.224 Ligands: TZD.6 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:E.193, C:E.193, C:Y.224, H2O.41

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 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: 4 interactions with chain B, 3 interactions with chain D, 1 interactions with chain A Hydrogen bonds: B:E.290, B:E.290, B:E.297, D:R.309 Water bridges: B:W.260, D:T.284, D:D.314, A:K.377 GOL.10: 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 9 PLIP interactions: 1 interactions with chain C, 4 interactions with chain B, 4 interactions with chain D Water bridges: C:K.377, B:T.284, B:D.314, D:W.260 Hydrogen bonds: B:T.284, B:R.309, D:E.290, D:T.294, D:E.297

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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