SMTL ID : 7zaz.1 (3 other biounits)

macrocyclase OphP with ZPP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

monomer

Ligands

1 x ZPR: N-BENZYLOXYCARBONYL-L-PROLYL-L-PROLINAL(Covalent)

ZPR.1: 13 residues within 4Å: Chain A: D.169, R.203, F.204, I.264, Y.499, F.502, S.580, N.581, F.617, W.621, Y.625, R.667, V.668 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:F.204, A:I.264, A:F.502, A:W.621, A:W.621, A:V.668 Hydrogen bonds: A:Y.499, A:N.581, A:R.667 pi-Stacking: A:F.617

2 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.2: 4 residues within 4Å: Chain A: R.33, P.35, Y.643, H.644 1 PLIP interactions: 1 interactions with chain A pi-Cation interactions: A:Y.643 DMS.3: 7 residues within 4Å: Chain A: A.234, F.262, I.264, T.616, F.617, A.619, S.620 2 PLIP interactions: 2 interactions with chain A Water bridges: A:A.619 pi-Cation interactions: A:F.262

7 x BCT: BICARBONATE ION(Non-functional Binders)

BCT.4: 6 residues within 4Å: Chain A: Y.521, R.522, R.573, L.727, T.728, Q.730 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.728, A:T.728 BCT.5: 6 residues within 4Å: Chain A: R.577, I.603, F.660, F.702, E.713, E.717 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.713 BCT.6: 5 residues within 4Å: Chain A: R.316, M.330, Y.338, F.363, V.365 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.316, A:R.316 BCT.7: 2 residues within 4Å: Chain A: T.491, R.573 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.570 BCT.8: 3 residues within 4Å: Chain A: F.638, H.644, N.645 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.644 BCT.9: 6 residues within 4Å: Chain A: I.206, S.266, V.267, Q.268, L.277, A.279 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.266 BCT.10: 2 residues within 4Å: Chain A: R.598, K.723 No protein-ligand interaction detected (PLIP)

3 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.11: 5 residues within 4Å: Chain A: S.87, A.88, K.90, Y.98, S.412 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.87, A:E.100, A:S.412 Water bridges: A:A.88, A:S.412 EDO.12: 7 residues within 4Å: Chain A: V.365, S.366, V.378, H.385, F.409, M.410, V.411 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.366, A:V.411, A:V.411 Water bridges: A:H.385, A:F.409 EDO.13: 2 residues within 4Å: Chain A: W.263, R.282 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:W.263 Water bridges: A:R.282

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Matabaro, E. et al., Molecular basis for the enzymatic macrocyclization of multiply backbone N-methylated peptides. Biorxiv (2022)

Release Date

2022-07-06

Peptides

Prolyl endopeptidase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
AAA

Prolyl endopeptidase

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