SMTL ID : 1wci.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.84 Å

Oligo State

hetero-2-2-mer

Ligands

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

CL.1: 3 residues within 4Å: Chain A: H.392 Chain D: K.329, W.330 Ligand excluded by PLIP CL.5: 3 residues within 4Å: Chain B: F.54, F.99, V.139 Ligand excluded by PLIP CL.9: 3 residues within 4Å: Chain B: K.329, W.330 Chain C: H.392 Ligand excluded by PLIP CL.13: 3 residues within 4Å: Chain D: F.54, F.99, V.139 Ligand excluded by PLIP

2 x WWF: C2-1-HYDROXY-3-METHYL-BUTYL-THIAMIN(Non-covalent)

WWF.2: 26 residues within 4Å: Chain A: F.85, Q.112, Y.113, R.114, 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 25 PLIP interactions: 22 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:G.192, A:E.193, A:G.194, A:A.195, A:N.222, D:Y.102 Water bridges: A:R.114, A:R.220, A:N.222, A:H.291 Salt bridges: A:R.114, A:R.220, A:H.291 pi-Stacking: D:Y.102 WWF.10: 26 residues within 4Å: Chain B: E.46, L.74, E.76, Q.98, Y.102, H.146 Chain C: F.85, Q.112, Y.113, R.114, 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.12 25 PLIP interactions: 23 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:G.192, C:E.193, C:G.194, C:A.195, C:E.198, C:N.222, C:N.222 Water bridges: C:R.114, C:R.220, C:N.222 Salt bridges: C:R.114, C:R.220, C:H.291 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 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:S.161, A:P.163, H2O.5 K.8: 7 residues within 4Å: Chain B: G.128, L.130, T.131, C.178, I.179, D.181, N.183 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:G.128, B:L.130, B:C.178, B:D.181, B:N.183 K.11: 4 residues within 4Å: Chain C: S.161, P.163, T.166, Q.167 3 PLIP interactions: 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:S.161, C:P.163, H2O.28 K.16: 7 residues within 4Å: Chain D: G.128, L.130, T.131, C.178, I.179, D.181, N.183 5 PLIP interactions: 5 interactions with chain D Metal complexes: D:G.128, D:L.130, D:C.178, D:D.181, D:N.183

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

MN.4: 5 residues within 4Å: Chain A: E.193, N.222, Y.224, A.225 Ligands: WWF.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.12: 5 residues within 4Å: Chain C: E.193, N.222, Y.224, A.225 Ligands: WWF.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.37

4 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, 5 interactions with chain B Hydrogen bonds: D:R.309, B:E.290, B:E.290, B:E.297 Water bridges: D:T.284, D:D.314, B:W.260, B:E.297 GOL.7: 5 residues within 4Å: Chain A: K.153, R.185 Chain B: V.88, T.89, F.125 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.185, A:R.185 Water bridges: A:H.156 GOL.14: 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: 4 interactions with chain B, 4 interactions with chain D Hydrogen bonds: B:T.284, B:R.309, D:E.290, D:T.294, D:E.297 Water bridges: B:T.284, B:D.314, D:W.260 GOL.15: 5 residues within 4Å: Chain C: K.153, R.185 Chain D: V.88, T.89, F.125 2 PLIP interactions: 2 interactions with chain C 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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