SMTL ID : 5qix.1

Covalent fragment group deposition -- Crystal Structure of OUTB2 in complex with PCM-0103007

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.39 Å

Oligo State

monomer

Ligands

1 x J5V: N-(3-phenylprop-2-yn-1-yl)acetamide(Covalent)

J5V.1: 11 residues within 4Å: Chain A: K.41, G.42, D.43, R.44, N.45, C.46, F.47, E.169, T.217, S.218, H.219 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:H.219 Hydrogen bonds: A:D.43, A:D.43, A:R.44, A:C.46, A:S.218 pi-Stacking: A:H.219

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

EDO.2: 7 residues within 4Å: Chain A: F.1, N.2, L.3, S.5, K.39, T.40, K.41 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:L.3 EDO.3: 6 residues within 4Å: Chain A: R.72, F.137, Q.180, A.181, L.182, S.183 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.72 Water bridges: A:R.72, A:S.183 EDO.4: 1 residues within 4Å: Chain A: H.88 1 PLIP interactions: 1 interactions with chain A Water bridges: A:R.91 EDO.5: 1 residues within 4Å: Chain A: N.95 No protein-ligand interaction detected (PLIP) EDO.6: 4 residues within 4Å: Chain A: E.19, N.20, R.21, R.24 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.19, A:N.20 EDO.7: 4 residues within 4Å: Chain A: S.109, S.111, S.112, K.115 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.109, A:S.109, A:K.115 EDO.8: 2 residues within 4Å: Chain A: N.78, A.82 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.82 Water bridges: A:N.78

3 x UNL: UNKNOWN LIGAND

UNL.9: 4 residues within 4Å: Chain A: D.124, Q.128 Ligands: UNL.10, UNL.11 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.124 UNL.10: 3 residues within 4Å: Chain A: Q.128, M.166 Ligands: UNL.9 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.128 UNL.11: 2 residues within 4Å: Chain A: H.125 Ligands: UNL.9 No protein-ligand interaction detected (PLIP)

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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