SMTL ID : 1v1m.1

CROSSTALK BETWEEN COFACTOR BINDING AND THE PHOSPHORYLATION LOOP CONFORMATION IN THE BCKD MACHINE

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

hetero-2-2-mer

Ligands

2 x TPP: THIAMINE DIPHOSPHATE(Non-covalent)

TPP.1: 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: CL.2, MN.5 23 PLIP interactions: 21 interactions with chain A, 2 interactions with chain D Hydrophobic interactions: A:A.225, A:I.226, A:I.226, 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.114, A:R.114, A:R.220, A:R.220, A:R.220, A:R.220, A:N.222, A:N.222, A:N.222 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: 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: CL.13, MN.16 24 PLIP interactions: 2 interactions with chain B, 22 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, C:Y.224 Water bridges: C:R.114, C:R.114, C:R.114, C:R.114, C:R.220, C:R.220, C:R.220, C:R.220, C:N.222 Salt bridges: C:R.114, C:R.220

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

CL.2: 4 residues within 4Å: Chain A: Y.113 Chain D: Y.102, H.146 Ligands: TPP.1 Ligand excluded by PLIP CL.3: 2 residues within 4Å: Chain A: E.76 Ligands: BEN.6 Ligand excluded by PLIP CL.7: 3 residues within 4Å: Chain B: K.329, W.330 Chain C: H.392 Ligand excluded by PLIP CL.13: 4 residues within 4Å: Chain B: Y.102, H.146 Chain C: Y.113 Ligands: TPP.12 Ligand excluded by PLIP CL.14: 2 residues within 4Å: Chain C: E.76 Ligands: BEN.17 Ligand excluded by PLIP CL.18: 3 residues within 4Å: Chain A: H.392 Chain D: K.329, W.330 Ligand excluded by PLIP

4 x K: POTASSIUM ION(Non-covalent)

K.4: 5 residues within 4Å: Chain A: Q.112, 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.4 K.11: 6 residues within 4Å: Chain B: G.128, L.130, T.131, C.178, 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.15: 5 residues within 4Å: Chain C: Q.112, 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.26 K.22: 6 residues within 4Å: Chain D: G.128, L.130, T.131, C.178, 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.5: 4 residues within 4Å: Chain A: E.193, N.222, Y.224 Ligands: TPP.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.13 MN.16: 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.35

2 x BEN: BENZAMIDINE(Non-functional Binders)

BEN.6: 8 residues within 4Å: Chain A: I.73, E.76, S.77, Q.80, R.82, M.346, F.349 Ligands: CL.3 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:F.349 Hydrogen bonds: A:I.73, A:S.77, A:Q.80 Water bridges: A:R.82 BEN.17: 8 residues within 4Å: Chain C: I.73, E.76, S.77, Q.80, R.82, M.346, F.349 Ligands: CL.14 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:F.349 Hydrogen bonds: C:I.73, C:S.77, C:Q.80 Water bridges: C:R.82

6 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: 4 interactions with chain D, 4 interactions with chain B Hydrogen bonds: D:T.284, D:R.309, B:E.290, B:E.297 Water bridges: D:D.314, D:D.314, B:W.260, B:E.297 GOL.9: 6 residues within 4Å: Chain A: L.108, K.153, R.185 Chain B: V.88, T.89, F.125 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.185, A:R.185 GOL.10: 6 residues within 4Å: Chain B: L.283, R.309, V.310, C.311, Y.313 Chain C: S.381 5 PLIP interactions: 2 interactions with chain C, 3 interactions with chain B Hydrogen bonds: C:S.381, C:S.381, B:R.309, B:C.311, B:C.311 GOL.19: 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: 4 interactions with chain D, 5 interactions with chain B Hydrogen bonds: D:T.294, D:E.297, B:T.284, B:T.284, B:R.309 Water bridges: D:W.260, D:E.298, B:T.284, B:D.314 GOL.20: 6 residues within 4Å: Chain C: L.108, 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 GOL.21: 6 residues within 4Å: Chain A: S.381 Chain D: L.283, R.309, V.310, C.311, Y.313 5 PLIP interactions: 3 interactions with chain D, 2 interactions with chain A Hydrogen bonds: D:R.309, D:C.311, D:C.311, A:S.381, A:S.381

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Li, J. et al., Cross-Talk between Thiamin Diphosphate Binding and Phosphorylation Loop Conformation in Human Branched-Chain Alpha-Keto Acid Decarboxylase/Dehydrogenase. J.Biol.Chem. (2004)

Release Date

2004-06-03

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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