SMTL ID : 7rv6.1

Crystal structure of the BCL6 BTB domain in complex with OICR-9288

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.68 Å

Oligo State

homo-dimer

Ligands

2 x 7SC: N-(3-chloropyridin-4-yl)-2-{4-oxo-2-[(2-phenylethyl)amino]-3,4-dihydro-7H-pyrrolo[2,3-d]pyrimidin-7-yl}acetamide(Non-covalent)

7SC.1: 14 residues within 4Å: Chain A: M.49, A.50, C.51, S.52, G.53, Y.56, Q.111, M.112, E.113, H.114 Chain B: N.19, R.22, L.23, R.26 7 PLIP interactions: 1 interactions with chain B, 6 interactions with chain A Hydrogen bonds: B:N.19, A:M.49, A:E.113 Hydrophobic interactions: A:Y.56, A:Y.56 Water bridges: A:Q.111, A:H.114 7SC.4: 14 residues within 4Å: Chain A: N.19, R.22, L.23, R.26 Chain B: M.49, A.50, C.51, S.52, G.53, Y.56, Q.111, M.112, E.113, H.114 7 PLIP interactions: 6 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:Y.56, B:Y.56 Hydrogen bonds: B:M.49, B:E.113, A:N.19 Water bridges: B:Q.111, B:H.114

2 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.2: 6 residues within 4Å: Chain A: I.7, Q.8, F.9, T.10 Chain B: H.114, T.118 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.10 pi-Cation interactions: A:F.9 DMS.5: 6 residues within 4Å: Chain A: H.114, T.118 Chain B: I.7, Q.8, F.9, T.10 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.10 pi-Cation interactions: B:F.9

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 12 residues within 4Å: Chain A: L.29, T.30, D.31, H.44, K.45, T.46 Chain B: L.29, D.31, H.44, K.45, T.46 Ligands: GOL.6 7 PLIP interactions: 2 interactions with chain B, 5 interactions with chain A Hydrogen bonds: B:L.29, B:T.46, A:K.45, A:T.46, A:T.46, A:T.46 Water bridges: A:D.31 GOL.6: 12 residues within 4Å: Chain A: L.29, D.31, H.44, K.45, T.46 Chain B: L.29, T.30, D.31, H.44, K.45, T.46 Ligands: GOL.3 6 PLIP interactions: 4 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:K.45, B:T.46, B:T.46, B:T.46, A:L.29, A:T.46

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Watson, I. et al., Structure of the BCL6 BTB domain. To Be Published

Release Date

2022-08-24

Peptides

Isoform 2 of B-cell lymphoma 6 protein: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Isoform 2 of B-cell lymphoma 6 protein

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