SMTL ID : 2vbb.1

Isopenicillin N synthase with substrate analogue ACOMP (35minutes oxygen exposure)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.40 Å

Oligo State

monomer

Ligands

1 x VAZ: N^6^-{(1R)-2-{[(1S,2R)-1-carboxy-2-hydroxy-2-(methylsulfanyl)ethyl]oxy}-1-[(oxidosulfanyl)methyl]-2-oxoethyl}-6-oxo-L-lysine(Non-covalent)

VAZ.1: 20 residues within 4Å: Chain A: R.87, Y.91, C.104, S.183, I.187, Y.189, F.211, H.214, D.216, L.223, Q.225, L.231, H.270, V.272, S.281, P.283, F.285, L.321, L.324 Ligands: FE2.2 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:F.285, A:L.321, A:L.324 Hydrogen bonds: A:Y.91, A:S.183, A:S.183, A:Y.189, A:Q.225, A:S.281, A:S.281 Water bridges: A:Y.91, A:Y.91, A:T.331 Salt bridges: A:R.87

1 x FE2: FE (II) ION(Non-covalent)

FE2.2: 4 residues within 4Å: Chain A: H.214, D.216, H.270 Ligands: VAZ.1 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.214, A:D.216, A:H.270, H2O.13

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

SO4.3: 4 residues within 4Å: Chain A: R.53, D.140, F.141, Q.144 7 PLIP interactions: 7 interactions with chain A Water bridges: A:R.53, A:R.53, A:R.53, A:R.53, A:F.141, A:F.141 Salt bridges: A:R.53 SO4.4: 1 residues within 4Å: Chain A: K.80 2 PLIP interactions: 2 interactions with chain A Water bridges: A:K.80 Salt bridges: A:K.80

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 4 residues within 4Å: Chain A: A.119, T.121, P.122, Y.290 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.119, A:Y.290

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ge, W. et al., Isopenicillin N Synthase Mediates Thiolate Oxidation to Sulfenate in a Depsipeptide Substrate Analogue: Implications for Oxygen Binding and a Link to Nitrile Hydratase?. J.Am.Chem.Soc. (2008)

Release Date

2008-07-29

Peptides

ISOPENICILLIN N SYNTHETASE: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

ISOPENICILLIN N SYNTHETASE

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