SMTL ID : 4jq9.1 (2 other biounits)

Dihydrolipoyl dehydrogenase of Escherichia coli pyruvate dehydrogenase complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.17 Å

Oligo State

homo-dimer

Ligands

13 x SO4: SULFATE ION(Non-functional Binders)

SO4.1: 3 residues within 4Å: Chain A: G.184, I.185, I.186 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:I.185, A:I.186 Water bridges: A:G.184, A:G.187, A:A.270 SO4.2: 4 residues within 4Å: Chain A: G.121, A.122, N.123, T.124 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.121, A:A.122, A:N.123, A:T.124 SO4.3: 2 residues within 4Å: Chain A: D.298, K.299 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.299 SO4.4: 4 residues within 4Å: Chain A: K.278, D.281, A.282, G.283 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:D.281, A:G.283 Water bridges: A:K.278, A:D.281, A:D.281, A:A.282 SO4.10: 2 residues within 4Å: Chain A: K.338, H.340 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:K.338, A:H.340 SO4.11: 5 residues within 4Å: Chain A: R.292, F.294, R.296, G.316, Q.317 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.317 Salt bridges: A:R.292, A:R.296 SO4.13: 3 residues within 4Å: Chain B: G.184, I.185, I.186 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:I.185, B:I.186 Water bridges: B:G.184, B:G.184, B:G.187 SO4.14: 2 residues within 4Å: Chain B: D.298, K.299 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:K.299 Water bridges: B:D.298, B:K.299 Salt bridges: B:K.299 SO4.15: 6 residues within 4Å: Chain A: K.61, N.417 Chain B: K.61, E.65, T.416, N.417 6 PLIP interactions: 4 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:N.417, B:N.417, A:N.417 Water bridges: B:R.386 Salt bridges: B:K.61, A:K.61 SO4.16: 4 residues within 4Å: Chain B: G.121, A.122, N.123, T.124 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:A.122, B:N.123, B:T.124 Water bridges: B:T.120 SO4.19: 5 residues within 4Å: Chain B: K.278, D.281, A.282, G.283, V.289 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:A.282, B:G.283 Water bridges: B:K.278, B:D.281, B:D.281, B:D.281, B:G.283, B:V.289 SO4.20: 2 residues within 4Å: Chain B: Y.38, N.39 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.39, B:N.39 SO4.21: 1 residues within 4Å: Chain B: K.244 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.245

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 8 residues within 4Å: Chain A: L.57, H.58, K.61, Y.352, T.353, E.354, E.356 Chain B: R.386 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:T.353, A:E.356, A:E.356, B:R.386, B:R.386 GOL.17: 8 residues within 4Å: Chain A: R.386 Chain B: L.57, H.58, K.61, Y.352, T.353, E.354, E.356 4 PLIP interactions: 1 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:R.386, B:T.353, B:E.356, B:E.356 GOL.18: 3 residues within 4Å: Chain B: K.338, K.339, H.340 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.339 Water bridges: B:K.338

2 x IMD: IMIDAZOLE(Non-covalent)

IMD.6: 5 residues within 4Å: Chain A: Y.38, G.43, V.44, N.47 Ligands: FAD.12 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:N.47 Water bridges: A:E.36, A:T.40, A:G.43, A:N.47 pi-Stacking: A:Y.38 IMD.7: 1 residues within 4Å: Chain A: E.369 No protein-ligand interaction detected (PLIP)

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

CL.8: 1 residues within 4Å: Chain A: E.245 Ligand excluded by PLIP CL.9: 1 residues within 4Å: Chain A: V.238 Ligand excluded by PLIP

2 x FAD: FLAVIN-ADENINE DINUCLEOTIDE(Non-covalent)

FAD.12: 38 residues within 4Å: Chain A: L.12, G.13, A.14, G.15, P.16, A.17, G.18, V.35, E.36, R.37, Y.38, G.43, V.44, C.45, V.48, G.49, C.50, K.54, G.115, L.116, G.117, A.144, A.145, G.146, S.165, I.186, R.273, L.280, G.312, D.313, M.319, L.320, A.321, H.322, Y.352 Chain B: H.445, P.446 Ligands: IMD.6 29 PLIP interactions: 27 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:V.44, A:I.186 Hydrogen bonds: A:A.14, A:G.15, A:A.17, A:G.18, A:R.37, A:R.37, A:V.44, A:C.45, A:K.54, A:G.117, A:G.117, A:S.147, A:D.313, A:M.319, A:A.321, A:H.322, A:H.322, B:H.445 Water bridges: A:R.37, A:R.37, A:G.43, A:G.146, A:D.313, A:I.314, A:Y.352, B:H.445 pi-Cation interactions: A:R.37 FAD.22: 36 residues within 4Å: Chain A: H.445, P.446 Chain B: L.12, G.13, A.14, G.15, P.16, A.17, G.18, E.36, R.37, Y.38, G.43, V.44, C.45, V.48, G.49, C.50, K.54, G.115, L.116, G.117, A.144, A.145, G.146, S.165, I.186, R.273, L.280, G.312, D.313, M.319, L.320, A.321, H.322, Y.352 31 PLIP interactions: 29 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:V.44, B:I.186, B:I.186 Hydrogen bonds: B:A.14, B:G.15, B:A.17, B:G.18, B:R.37, B:R.37, B:V.44, B:C.45, B:K.54, B:G.117, B:G.117, B:S.147, B:D.313, B:M.319, B:A.321, B:H.322, A:H.445 Water bridges: B:A.14, B:R.37, B:R.37, B:G.43, B:K.118, B:G.146, B:D.313, B:I.314, B:Y.352, A:H.445 pi-Cation interactions: B:R.37

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tietzel, M. et al., Dihydrolipoyl dehydrogenase of Escherichia coli pyruvate dehydrogenase complex. TO BE PUBLISHED

Release Date

2014-04-02

Peptides

Dihydrolipoyl dehydrogenase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Dihydrolipoyl dehydrogenase

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