SMTL ID : 4nsy.1

Wild-type lysobacter enzymogenes lysc endoproteinase covalently inhibited by TLCK

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.10 Å

Oligo State

homo-dimer

Ligands

2 x 2OY: N-[(2S,3S)-7-amino-1-chloro-2-hydroxyheptan-3-yl]-4-methylbenzenesulfonamide (Bound Form)(Covalent)

2OY.1: 23 residues within 4Å: Chain A: C.36, H.57, C.58, Y.169, T.189, E.190, P.191, G.192, S.193, S.194, L.209, H.210, G.211, G.212, P.213, S.214, D.225 Chain B: A.110, A.111, D.113, Y.169, H.210 Ligands: CL.2 11 PLIP interactions: 10 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:H.57 Hydrogen bonds: A:G.192, A:S.194, A:H.210, A:S.214, A:S.214, A:D.225 Water bridges: A:Y.169, A:G.212, B:H.210 pi-Stacking: A:H.57 2OY.4: 24 residues within 4Å: Chain A: A.110, A.111, D.113, Y.169, H.177, H.210 Chain B: C.36, H.57, C.58, Y.169, T.189, E.190, P.191, G.192, S.193, S.194, L.209, H.210, G.211, G.212, P.213, S.214, D.225 Ligands: CL.2 10 PLIP interactions: 9 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:H.57 Hydrogen bonds: B:G.192, B:S.194, B:H.210, B:S.214, B:D.225 Water bridges: B:Y.169, B:G.212, A:H.210 pi-Stacking: B:H.57

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.2: 6 residues within 4Å: Chain A: H.57, H.210 Chain B: H.57, H.210 Ligands: 2OY.1, 2OY.4 Ligand excluded by PLIP CL.3: 1 residues within 4Å: Chain A: N.151 Ligand excluded by PLIP

2 x CA: CALCIUM ION(Non-covalent)

CA.5: 3 residues within 4Å: Chain B: S.240, R.243, D.246 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:D.246, H2O.31, H2O.31, H2O.34, H2O.36 CA.6: 1 residues within 4Å: Chain B: N.151 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Asztalos, P. et al., Atomic resolution structure of a lysine-specific endoproteinase from Lysobacter enzymogenes suggests a hydroxyl group bound to the oxyanion hole. Acta Crystallogr.,Sect.D (2014)

Release Date

2014-04-23

Peptides

Lysyl endopeptidase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Lysyl endopeptidase