SMTL ID : 4jq9.3 (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

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

SO4.1: 5 residues within 4Å: Chain A: K.278, D.281, A.282, G.283, V.289 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:G.283 Water bridges: A:L.280, A:L.280, A:D.281, A:A.282, A:A.282, A:K.284, A:V.289 SO4.2: 2 residues within 4Å: Chain A: D.298, K.299 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.299 Salt bridges: A:K.299 SO4.3: 3 residues within 4Å: Chain A: G.184, I.185, I.186 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:I.185, A:I.186 Water bridges: A:G.184, A:R.273 SO4.4: 6 residues within 4Å: Chain A: K.61, E.65, N.417 Chain B: H.58, K.61, N.417 6 PLIP interactions: 3 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:N.417, A:N.417, A:N.417 Water bridges: B:N.417 Salt bridges: B:K.61, A:K.61 SO4.5: 2 residues within 4Å: Chain A: K.338, H.340 4 PLIP interactions: 4 interactions with chain A Water bridges: A:K.338, A:K.339 Salt bridges: A:K.338, A:H.340 SO4.8: 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:A.122, A:N.123, A:N.123, A:T.124 SO4.9: 1 residues within 4Å: Chain A: R.263 2 PLIP interactions: 2 interactions with chain A Water bridges: A:R.263 Salt bridges: A:R.263 SO4.12: 4 residues within 4Å: Chain B: G.184, I.185, I.186, I.271 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:I.185, B:I.186 Water bridges: B:G.184, B:G.184, B:G.187, B:A.270, B:R.273 SO4.17: 2 residues within 4Å: Chain B: D.298, K.299 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.299 Salt bridges: B:K.299

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 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: 2 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:R.386, B:R.386, A:T.353, A:E.356, A:E.356 GOL.7: 6 residues within 4Å: Chain A: R.37, Y.38, G.43, V.44, N.47 Ligands: FAD.10 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.37, A:G.43 Water bridges: A:S.147, A:N.276 GOL.13: 8 residues within 4Å: Chain A: R.386 Chain B: L.57, H.58, K.61, Y.352, T.353, E.354, E.356 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:R.386, B:Y.352, B:E.356 GOL.14: 7 residues within 4Å: Chain B: G.182, V.204, E.205, M.206, K.237, V.238, I.271 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:V.204, B:M.206, B:V.238, B:V.238

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

FAD.10: 40 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, S.53, K.54, G.115, L.116, G.117, A.144, A.145, G.146, S.147, 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: GOL.7 29 PLIP interactions: 26 interactions with chain A, 3 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, B:H.445 Water bridges: A:R.37, A:R.37, A:G.43, A:G.146, A:D.313, A:I.314, A:G.324, B:H.445, B:H.445 pi-Cation interactions: A:R.37 FAD.11: 37 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, V.35, E.36, R.37, G.43, V.44, C.45, V.48, G.49, C.50, S.53, 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 28 PLIP interactions: 2 interactions with chain A, 26 interactions with chain B Hydrogen bonds: A:H.445, 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:D.313, B:M.319, B:A.321, B:H.322 Water bridges: A:H.445, B:A.14, B:G.43, B:G.146, B:S.147, B:S.147, B:D.313, B:I.314, B:Y.352 Hydrophobic interactions: B:V.44, B:I.186 pi-Cation interactions: B:R.37

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

CL.15: 1 residues within 4Å: Chain B: R.263 Ligand excluded by PLIP CL.16: 1 residues within 4Å: Chain B: G.283 Ligand excluded by PLIP

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
D

B
F

Dihydrolipoyl dehydrogenase

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