SMTL ID : 7poy.1

Spin labeled IPNS S55C variant in complex with Fe, ACV and NO

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

monomer

Ligands

1 x FE: FE (III) ION(Non-covalent)

FE.1: 5 residues within 4Å: Chain A: H.214, D.216, H.270 Ligands: ACV.2, NO.3 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.214, A:D.216, A:H.270, H2O.2

1 x ACV: L-D-(A-AMINOADIPOYL)-L-CYSTEINYL-D-VALINE(Non-covalent)

ACV.2: 24 residues within 4Å: Chain A: R.87, Y.91, C.104, L.106, S.183, V.185, I.187, Y.189, F.211, H.214, D.216, L.223, Q.225, L.231, V.272, S.281, P.283, F.285, N.287, L.321, L.324, T.331 Ligands: FE.1, NO.3 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:P.283, A:F.285, A:F.285, A:L.321 Hydrogen bonds: A:Y.91, A:S.183, A:Y.189, A:Q.225, A:S.281, A:S.281 Water bridges: A:R.279, A:N.287, A:T.331 Salt bridges: A:R.87

1 x NO: NITRIC OXIDE(Non-covalent)

NO.3: 7 residues within 4Å: Chain A: F.211, H.214, L.231, H.270, V.272 Ligands: FE.1, ACV.2 No protein-ligand interaction detected (PLIP)

1 x 81T: ~{N}-[(3~{R})-2,2,5,5-tetramethyl-1-oxidanyl-pyrrolidin-3-yl]ethanamide(Covalent)

81T.4: 8 residues within 4Å: Chain A: V.51, Q.52, C.55, Y.224, S.226, D.246, T.247, Q.280 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:V.51, A:D.246, A:T.247 Hydrogen bonds: A:C.55, A:Y.224 Water bridges: A:D.246 Salt bridges: A:D.246

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

SO4.5: 3 residues within 4Å: Chain A: R.37, Y.264, R.300 6 PLIP interactions: 6 interactions with chain A Water bridges: A:R.37, A:N.263, A:N.263, A:R.300 Salt bridges: A:R.37, A:R.300 SO4.6: 2 residues within 4Å: Chain A: D.205, G.206 No protein-ligand interaction detected (PLIP) SO4.7: 2 residues within 4Å: Chain A: K.305, S.306 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.306 SO4.8: 3 residues within 4Å: Chain A: P.16, A.24, R.27 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.27

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Rabe, P. et al., Spectroscopic studies reveal details of substrate-induced conformational changes distant from the active site in isopenicillin N synthase. J.Biol.Chem. (2022)

Release Date

2022-07-20

Peptides

Isopenicillin N synthase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Isopenicillin N synthase

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