SMTL ID : 1v11.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

hetero-2-2-mer

Ligands

4 x K: POTASSIUM ION(Non-covalent)

K.1: 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.10: 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.16 K.14: 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.24 K.23: 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.36

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

MN.2: 4 residues within 4Å: Chain A: E.193, N.222, Y.224 Ligands: TPP.8 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.193, A:E.193, A:Y.224, H2O.12 MN.15: 4 residues within 4Å: Chain C: E.193, N.222, Y.224 Ligands: TPP.21 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:E.193, C:E.193, C:Y.224, H2O.32

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

CL.3: 4 residues within 4Å: Chain B: Y.102, H.146 Chain C: Y.113 Ligands: TPP.21 Ligand excluded by PLIP CL.4: 3 residues within 4Å: Chain B: K.329, W.330 Chain C: H.392 Ligand excluded by PLIP CL.5: 1 residues within 4Å: Chain B: R.55 Ligand excluded by PLIP CL.6: 2 residues within 4Å: Chain A: Q.351, R.354 Ligand excluded by PLIP CL.7: 2 residues within 4Å: Chain A: E.76 Ligands: BEN.9 Ligand excluded by PLIP CL.16: 4 residues within 4Å: Chain A: Y.113 Chain D: Y.102, H.146 Ligands: TPP.8 Ligand excluded by PLIP CL.17: 3 residues within 4Å: Chain A: H.392 Chain D: K.329, W.330 Ligand excluded by PLIP CL.18: 1 residues within 4Å: Chain D: R.55 Ligand excluded by PLIP CL.19: 2 residues within 4Å: Chain C: Q.351, R.354 Ligand excluded by PLIP CL.20: 2 residues within 4Å: Chain C: E.76 Ligands: BEN.22 Ligand excluded by PLIP

2 x TPP: THIAMINE DIPHOSPHATE(Non-covalent)

TPP.8: 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: MN.2, CL.16 21 PLIP interactions: 19 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:G.194, A:A.195 Water bridges: A:R.114, A:R.114, A:R.114, A:R.114, A:E.193, A:R.220, A:R.220, A:R.220, A:R.220, A:N.222 Salt bridges: A:R.114, A:R.220 pi-Stacking: D:Y.102 TPP.21: 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.3, MN.15 24 PLIP interactions: 22 interactions with chain C, 2 interactions with chain B Hydrophobic interactions: C:A.225, C:I.226, C:I.226, B:Y.102 Hydrogen bonds: C:S.162, C:L.164, C:G.192, C:G.194, C:A.195, C:N.222, C:Y.224 Water bridges: C:R.114, C:R.114, C:R.114, C:R.114, C:E.193, C:R.220, C:R.220, C:R.220, C:R.220, C:N.222 Salt bridges: C:R.114, C:R.220 pi-Stacking: B:Y.102

2 x BEN: BENZAMIDINE(Non-functional Binders)

BEN.9: 8 residues within 4Å: Chain A: I.73, E.76, S.77, Q.80, R.82, M.346, F.349 Ligands: CL.7 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:F.349 Hydrogen bonds: A:I.73, A:Q.80 Water bridges: A:R.82 BEN.22: 8 residues within 4Å: Chain C: I.73, E.76, S.77, Q.80, R.82, M.346, F.349 Ligands: CL.20 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:F.349 Hydrogen bonds: C:I.73, C:Q.80 Water bridges: C:R.82

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.11: 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 9 PLIP interactions: 3 interactions with chain A, 3 interactions with chain D, 3 interactions with chain B Water bridges: A:Q.374, A:K.377, A:Q.378, D:T.284, B:W.260 Hydrogen bonds: D:T.284, D:R.309, B:E.290, B:E.297 GOL.12: 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 Hydrogen bonds: B:V.88, A:R.185, A:R.185 GOL.13: 6 residues within 4Å: Chain B: L.283, R.309, V.310, C.311, Y.313 Chain C: S.381 7 PLIP interactions: 4 interactions with chain B, 3 interactions with chain C Hydrogen bonds: B:R.309, B:C.311, C:S.381, C:S.381 Water bridges: B:C.311, B:K.331, C:Q.378 GOL.24: 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: 4 interactions with chain B, 4 interactions with chain D, 2 interactions with chain C Hydrogen bonds: B:T.284, B:T.284, B:R.309, D:T.294, D:E.297 Water bridges: B:T.284, D:W.260, D:E.298, C:K.377, C:Q.378 GOL.25: 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 Hydrogen bonds: D:V.88, C:R.185, C:R.185 GOL.26: 6 residues within 4Å: Chain A: S.381 Chain D: L.283, R.309, V.310, C.311, Y.313 7 PLIP interactions: 3 interactions with chain A, 4 interactions with chain D Hydrogen bonds: A:S.381, A:S.381, D:R.309, D:C.311 Water bridges: A:Q.378, D:C.311, D:K.331

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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