SMTL ID : 5oxd.1

Complex of a C. perfringens O-GlcNAcase with a fragment hit

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

monomer

Ligands

22 x CD: CADMIUM ION(Non-covalent)(Non-functional Binders)

CD.1: 3 residues within 4Å: Chain A: E.23, N.422, D.424 Ligand excluded by PLIP CD.2: 1 residues within 4Å: Chain A: D.30 Ligand excluded by PLIP CD.3: 2 residues within 4Å: Chain A: L.40, E.43 Ligand excluded by PLIP CD.4: 3 residues within 4Å: Chain A: E.45, E.80, D.83 Ligand excluded by PLIP CD.5: 1 residues within 4Å: Chain A: D.84 Ligand excluded by PLIP CD.6: 4 residues within 4Å: Chain A: D.89, T.96, E.117 Ligands: CD.19 Ligand excluded by PLIP CD.7: 1 residues within 4Å: Chain A: D.111 Ligand excluded by PLIP CD.8: 3 residues within 4Å: Chain A: D.122, K.222, D.224 Ligand excluded by PLIP CD.9: 1 residues within 4Å: Chain A: E.142 Ligand excluded by PLIP CD.10: 3 residues within 4Å: Chain A: R.236, E.244, H.248 Ligand excluded by PLIP CD.11: 2 residues within 4Å: Chain A: E.254, D.258 Ligand excluded by PLIP CD.12: 1 residues within 4Å: Chain A: E.334 Ligand excluded by PLIP CD.13: 1 residues within 4Å: Chain A: D.360 Ligand excluded by PLIP CD.14: 1 residues within 4Å: Chain A: H.385 Ligand excluded by PLIP CD.15: 2 residues within 4Å: Chain A: D.446, R.503 Ligand excluded by PLIP CD.16: 2 residues within 4Å: Chain A: D.429, N.433 Ligand excluded by PLIP CD.17: 2 residues within 4Å: Chain A: D.89 Ligands: CD.19 Ligand excluded by PLIP CD.18: 1 residues within 4Å: Chain A: D.373 Ligand excluded by PLIP CD.19: 7 residues within 4Å: Chain A: E.80, V.81, D.83, D.89, E.117 Ligands: CD.6, CD.17 Ligand excluded by PLIP CD.20: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CD.21: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CD.22: 1 residues within 4Å: Chain A: E.522 Ligand excluded by PLIP

1 x B2W: 5-(trifluoromethyl)-2,3-dihydro-1~{H}-1,4-diazepine(Non-covalent)

B2W.23: 3 residues within 4Å: Chain A: Y.161, D.373, Y.374 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.373

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Borodkin, V.S. et al., O-GlcNAcase Fragment Discovery with Fluorescence Polarimetry. ACS Chem. Biol. (2018)

Release Date

2018-05-16

Peptides

O-GlcNAcase NagJ: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

O-GlcNAcase NagJ