SMTL ID : 2bew.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.79 Å

Oligo State

hetero-2-2-mer

Ligands

2 x ALA- TYR- ARG: PEPTIDE ALA-TYR-ARG(Non-covalent)

ALA-TYR-ARG.1: 12 residues within 4Å: Chain A: I.226, S.294, D.295 Chain D: F.50, G.51, G.52, V.53, F.54, R.55, V.58, F.99, R.195 12 PLIP interactions: 10 interactions with chain D, 2 interactions with chain A Hydrophobic interactions: D:V.53, D:F.54, D:F.54, D:F.99 Hydrogen bonds: D:F.50, D:G.52, D:V.53, D:R.195 Water bridges: D:R.195, A:H.291, A:S.292 pi-Cation interactions: D:F.50 ALA-TYR-ARG.10: 12 residues within 4Å: Chain B: F.50, G.51, G.52, V.53, F.54, R.55, V.58, F.99, R.195 Chain C: I.226, S.294, D.295 10 PLIP interactions: 9 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: B:V.53, B:F.54, B:F.54, B:F.99 Hydrogen bonds: B:F.50, B:G.52, B:V.53 Water bridges: B:R.195, C:H.291 pi-Cation interactions: B:F.50

2 x THW: C2-1-HYDROXYPHENYL-THIAMIN DIPHOSPHATE(Non-covalent)

THW.2: 28 residues within 4Å: Chain A: F.85, M.87, Q.112, Y.113, R.114, M.146, H.149, 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, H.146 Ligands: MN.4 22 PLIP interactions: 19 interactions with chain A, 3 interactions with chain D Hydrophobic interactions: A:F.85, A:Y.113, A:Y.113, A:L.164, A:I.226, A:I.226, D:Y.102 Hydrogen bonds: A:Q.112, A:Y.113, A:S.162, A:G.192, A:E.193, A:G.194, A:A.195, A:H.291, D:Y.102 Water bridges: A:R.114, A:R.220, A:N.222 Salt bridges: A:R.114, A:R.220 pi-Stacking: D:Y.102 THW.11: 28 residues within 4Å: Chain B: E.46, L.74, E.76, Q.98, Y.102, H.146 Chain C: F.85, M.87, Q.112, Y.113, R.114, M.146, H.149, 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.13 23 PLIP interactions: 21 interactions with chain C, 2 interactions with chain B Hydrophobic interactions: C:F.85, C:Y.113, C:Y.113, C:L.164, C:I.226, C:I.226, B:Y.102 Hydrogen bonds: C:Q.112, C:Y.113, 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.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.3: 4 residues within 4Å: Chain A: 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.5 K.6: 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.20 K.12: 4 residues within 4Å: Chain C: 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.29 K.15: 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.44

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

MN.4: 4 residues within 4Å: Chain A: E.193, N.222, Y.224 Ligands: THW.2 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.13: 4 residues within 4Å: Chain C: E.193, N.222, Y.224 Ligands: THW.11 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:E.193, C:E.193, C:Y.224, H2O.38

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

CL.5: 3 residues within 4Å: Chain A: H.392 Chain D: K.329, W.330 Ligand excluded by PLIP CL.7: 3 residues within 4Å: Chain B: F.54, F.99, V.139 Ligand excluded by PLIP CL.14: 3 residues within 4Å: Chain B: K.329, W.330 Chain C: H.392 Ligand excluded by PLIP CL.16: 3 residues within 4Å: Chain D: F.54, F.99, V.139 Ligand excluded by PLIP

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.8: 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: 2 interactions with chain A, 4 interactions with chain B, 2 interactions with chain D Water bridges: A:K.377, A:Q.378, B:W.260, D:T.284 Hydrogen bonds: B:E.290, B:E.290, B:E.297, D:R.309 GOL.9: 5 residues within 4Å: Chain A: K.153, R.185 Chain B: V.88, T.89, F.125 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Water bridges: B:L.124 Hydrogen bonds: A:R.185, A:R.185 GOL.17: 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 10 PLIP interactions: 5 interactions with chain D, 2 interactions with chain C, 3 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, D:E.298, C:K.377, C:Q.378, B:T.284 GOL.18: 5 residues within 4Å: Chain C: K.153, R.185 Chain D: V.88, T.89, F.125 3 PLIP interactions: 1 interactions with chain D, 2 interactions with chain C Water bridges: D:L.124 Hydrogen bonds: C:R.185, C:R.185

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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