SMTL ID : 5xwv.1

Substrate-bound Structure of a Ketoreductase from the Second Module of the amphotericin Polyketide Synthases

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-dimer

Ligands

2 x NDP: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE(Non-covalent)

NDP.1: 28 residues within 4Å: Chain A: G.246, T.248, G.249, G.250, I.251, S.271, R.272, R.273, C.299, D.300, A.301, S.326, A.327, G.328, V.329, A.350, K.351, F.373, S.374, S.375, Y.388, W.414, G.415, T.416, W.417, G.421, M.422 Ligands: 8H6.2 23 PLIP interactions: 23 interactions with chain A Hydrophobic interactions: A:I.251, A:W.414 Hydrogen bonds: A:G.246, A:G.250, A:I.251, A:R.272, A:R.273, A:D.300, A:D.300, A:A.301, A:S.326, A:G.328, A:K.351, A:Y.388, A:W.417, A:M.422 Water bridges: A:G.252, A:S.271, A:R.273, A:G.421, A:A.423 Salt bridges: A:R.272, A:R.273 NDP.3: 29 residues within 4Å: Chain B: G.246, T.248, G.249, G.250, I.251, S.271, R.272, R.273, C.299, D.300, A.301, S.326, A.327, G.328, V.329, A.350, K.351, F.373, S.374, S.375, Y.388, W.414, G.415, T.416, W.417, G.421, M.422, A.423 Ligands: 8H6.4 21 PLIP interactions: 21 interactions with chain B Hydrophobic interactions: B:W.414 Hydrogen bonds: B:G.246, B:T.248, B:G.250, B:I.251, B:R.272, B:R.273, B:D.300, B:A.301, B:S.326, B:G.328, B:K.351, B:W.417, B:M.422, B:A.423 Water bridges: B:S.271, B:R.273, B:S.326, B:G.421 Salt bridges: B:R.272, B:R.273

2 x 8H6: S-[2-[3-[[(2R)-3,3-dimethyl-2,4-bis(oxidanyl)butanoyl]amino]propanoylamino]ethyl] (2R)-2-methyl-3-oxidanylidene-pentanethioate(Non-covalent)

8H6.2: 16 residues within 4Å: Chain A: L.173, W.380, G.381, S.382, G.383, Q.385, Y.388, G.415, M.422, V.428, L.432, Q.435, F.470, A.473, F.474 Ligands: NDP.1 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:L.173, A:M.422, A:V.428, A:F.474 Hydrogen bonds: A:S.382, A:G.383, A:Q.435, A:Q.435 Water bridges: A:G.376, A:A.377 8H6.4: 16 residues within 4Å: Chain B: L.173, W.380, G.381, S.382, G.383, Q.385, Y.388, G.415, M.422, R.431, L.432, Q.435, F.470, A.473, F.474 Ligands: NDP.3 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:L.173, B:M.422, B:F.470, B:F.474 Hydrogen bonds: B:G.381, B:S.382, B:G.383, B:Y.388, B:Q.435, B:Q.435 Water bridges: B:G.376, B:A.377

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Liu, C. et al., Substrate-bound structures of a ketoreductase from amphotericin modular polyketide synthase. J. Struct. Biol. (2018)

Release Date

2018-06-06

Peptides

AmphB: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

AmphB

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