SMTL ID : 5ae3.2 (1 other biounit)

Ether Lipid-Generating Enzyme AGPS in complex with antimycin A

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.18 Å

Oligo State

homo-dimer

Ligands

2 x AWB: [(2R,3S,6S,7R,8R)-3-[(3-formamido-2-oxidanyl-phenyl)carbonylamino]-8-hexyl-2,6-dimethyl-4,9-bis(oxidanylidene)-1,5-dioxonan-7-yl] 3-methylbutanoate(Non-covalent)

AWB.1: 19 residues within 4Å: Chain A: F.128, W.131, I.132, F.136, R.419, M.421, Q.425, F.428, T.467, G.504, Y.505, I.511, M.514, G.518, E.526, S.527, L.562, R.566, Y.580 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:F.128, A:F.128, A:I.132, A:Q.425, A:F.428, A:F.428, A:I.511, A:Y.580 Hydrogen bonds: A:R.419, A:T.467, A:G.504, A:R.566, A:R.566 AWB.4: 23 residues within 4Å: Chain B: F.128, W.131, I.132, F.136, R.419, M.421, Q.425, F.428, G.429, T.467, G.504, Y.505, L.507, I.511, A.512, M.514, R.515, G.518, G.525, E.526, L.562, R.566, Y.580 18 PLIP interactions: 18 interactions with chain B Hydrophobic interactions: B:F.128, B:F.128, B:W.131, B:I.132, B:F.428, B:F.428, B:I.511, B:R.515, B:R.515, B:Y.580, B:Y.580 Hydrogen bonds: B:R.419, B:Q.425, B:G.504, B:R.566, B:R.566 Water bridges: B:R.419, B:R.419

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

FAD.2: 35 residues within 4Å: Chain A: W.96, H.189, P.234, I.235, G.236, G.237, G.238, T.239, S.240, V.241, G.244, L.245, T.260, A.280, P.302, D.303, S.304, S.308, T.309, G.311, G.312, W.313, S.315, T.316, A.318, S.319, E.368, G.369, G.372, V.373, I.374, A.512, H.616, N.654, N.656 31 PLIP interactions: 31 interactions with chain A Hydrophobic interactions: A:W.96, A:H.189, A:V.241, A:D.303, A:A.512 Hydrogen bonds: A:G.236, A:G.237, A:G.238, A:T.239, A:T.239, A:S.240, A:D.303, A:S.304, A:S.304, A:T.309, A:S.315, A:T.316, A:S.319, A:S.319, A:I.374, A:I.374, A:N.654, A:N.656 Water bridges: A:T.309, A:G.312, A:T.316, A:T.316, A:G.369, A:H.617 pi-Cation interactions: A:H.616, A:H.617 FAD.5: 34 residues within 4Å: Chain B: W.96, H.189, P.234, I.235, G.236, G.237, G.238, T.239, S.240, V.241, G.244, L.245, T.260, P.302, D.303, S.304, S.308, T.309, G.311, G.312, W.313, S.315, T.316, A.318, S.319, E.368, G.369, G.372, V.373, I.374, A.512, H.616, N.654, N.656 32 PLIP interactions: 32 interactions with chain B Hydrophobic interactions: B:W.96, B:H.189, B:D.303, B:A.512 Hydrogen bonds: B:G.236, B:G.237, B:G.238, B:T.239, B:T.239, B:T.239, B:S.240, B:G.244, B:D.303, B:S.304, B:S.304, B:T.309, B:S.315, B:S.319, B:S.319, B:G.369, B:I.374, B:I.374, B:N.654, B:N.656 Water bridges: B:T.260, B:D.303, B:G.312, B:T.316, B:T.316, B:H.617 pi-Cation interactions: B:H.616, B:H.617

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

SO4.3: 4 residues within 4Å: Chain A: K.323, Y.571, D.572 Chain B: K.380 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:D.572 Water bridges: A:K.323, A:K.323, A:A.573 Salt bridges: A:K.323, B:K.380 SO4.6: 5 residues within 4Å: Chain A: K.380 Chain B: K.323, T.570, Y.571, D.572 6 PLIP interactions: 1 interactions with chain A, 5 interactions with chain B Salt bridges: A:K.380, B:K.323 Hydrogen bonds: B:T.570, B:D.572 Water bridges: B:T.570, B:A.573

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Piano, V. et al., Discovery of Inhibitors for the Ether Lipid-Generating Enzyme Agps as Anti-Cancer Agents. Acs Chem.Biol. (2015)

Release Date

2015-09-09

Peptides

ALKYLDIHYDROXYACETONEPHOSPHATE SYNTHASE, PEROXISOMAL: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

ALKYLDIHYDROXYACETONEPHOSPHATE SYNTHASE, PEROXISOMAL

Related Entries With Identical Sequence