SMTL ID : 5qiv.1

Covalent fragment group deposition -- Crystal Structure of OUTB2 in complex with PCM-0102998

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.39 Å

Oligo State

monomer

Ligands

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

EDO.1: 3 residues within 4Å: Chain A: R.33, Q.187, Y.212 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.33, A:Q.187 Water bridges: A:Q.187 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 EDO.3: 4 residues within 4Å: Chain A: Q.128, L.132, E.164, P.165 1 PLIP interactions: 1 interactions with chain A Water bridges: A:E.164 EDO.4: 3 residues within 4Å: Chain A: E.71, R.72, Q.75 3 PLIP interactions: 3 interactions with chain A Water bridges: A:R.72, A:R.72, A:Q.75 EDO.5: 4 residues within 4Å: Chain A: E.6, K.7, R.38, L.114 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.38, A:R.38

1 x J5P: N'-acetyl-2-[(3R)-1,1-dioxo-1lambda~6~-thiolan-3-yl]acetohydrazide(Covalent)

J5P.6: 12 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, Y.220 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:Y.220 Hydrogen bonds: A:D.43, A:D.43, A:R.44, A:C.46, A:E.169, A:T.217, A:S.218

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

UNL.7: 5 residues within 4Å: Chain A: D.124, H.125 Ligands: UNL.8, UNL.9, UNL.11 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.124 UNL.8: 4 residues within 4Å: Chain A: H.125 Ligands: UNL.7, UNL.9, UNL.10 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.125 UNL.9: 4 residues within 4Å: Ligands: UNL.7, UNL.8, UNL.10, UNL.11 No protein-ligand interaction detected (PLIP) UNL.10: 4 residues within 4Å: Chain A: F.93 Ligands: UNL.8, UNL.9, UNL.11 No protein-ligand interaction detected (PLIP) UNL.11: 5 residues within 4Å: Chain A: Q.128, M.166 Ligands: UNL.7, UNL.9, UNL.10 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.128

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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