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

macrocyclase OphP with ZPP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

monomer

Ligands

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

BCT.1: 5 residues within 4Å: Chain A: K.78, W.81, N.82, G.104, L.711 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.104 BCT.2: 3 residues within 4Å: Chain A: R.33, P.35, Y.643 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.643 BCT.3: 5 residues within 4Å: Chain A: F.133, F.134, N.135, L.138, P.181 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.135 BCT.4: 5 residues within 4Å: Chain A: R.84, F.86, L.123, T.124, E.125 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.125 Water bridges: A:S.452 BCT.5: 3 residues within 4Å: Chain A: Q.550, Q.592, K.639 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.639, A:K.639

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

ZPR.6: 11 residues within 4Å: Chain A: R.203, F.204, I.264, Y.499, F.502, S.580, N.581, I.606, F.617, W.621, R.667 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:F.204, A:I.264, A:F.502, A:I.606, A:F.617, A:W.621, A:W.621 Hydrogen bonds: A:N.581

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 5 residues within 4Å: Chain A: V.365, S.366, F.409, M.410, V.411 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.366, A:V.411, A:V.411

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

EDO.8: 5 residues within 4Å: Chain A: S.87, A.88, K.90, F.150, S.412 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.87, A:A.88, A:S.412 Water bridges: A:A.88 EDO.9: 6 residues within 4Å: Chain A: L.495, T.514, R.577, T.714, E.717, Y.718 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.577, A:T.714

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
CCC

Prolyl endopeptidase

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