SMTL ID : 5qiu.1

Covalent fragment group deposition -- Crystal Structure of OUTB2 in complex with PCM-0103011

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.56 Å

Oligo State

monomer

Ligands

1 x J5M: N-{3-[3-(trifluoromethyl)phenyl]prop-2-yn-1-yl}acetamide(Covalent)

J5M.1: 9 residues within 4Å: Chain A: G.42, D.43, R.44, N.45, C.46, F.47, T.217, S.218, H.219 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:H.219 Hydrogen bonds: A:D.43, A:D.43, A:R.44, A:N.45, A:C.46, A:S.218 pi-Stacking: A:H.219

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

EDO.2: 8 residues within 4Å: Chain A: F.1, N.2, L.3, I.4, S.5, K.39, T.40, K.41 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:L.3

5 x UNL: UNKNOWN LIGAND(Non-functional Binders)

UNL.3: 5 residues within 4Å: Chain A: D.195 Ligands: UNL.4, UNL.5, UNL.6, UNL.7 2 PLIP interactions: 2 interactions with chain A Water bridges: A:R.25, A:D.195 UNL.4: 5 residues within 4Å: Chain A: R.25 Ligands: UNL.3, UNL.5, UNL.6, UNL.7 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.25 UNL.5: 3 residues within 4Å: Ligands: UNL.3, UNL.4, UNL.6 3 PLIP interactions: 3 interactions with chain A Water bridges: A:R.25, A:E.29, A:E.29 UNL.6: 4 residues within 4Å: Ligands: UNL.3, UNL.4, UNL.5, UNL.7 No protein-ligand interaction detected (PLIP) UNL.7: 6 residues within 4Å: Chain A: D.195, T.196, A.197 Ligands: UNL.3, UNL.4, UNL.6 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.195

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sethi, R. et al., Covalent fragment group deposition. To Be Published

Release Date

2019-12-18

Peptides

Ubiquitin thioesterase OTUB2: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Ubiquitin thioesterase OTUB2

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