SMTL ID : 7lzr.2 (1 other biounit)

Crystal structure of the BCL6 BTB domain in complex with OICR-10256

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.34 Å

Oligo State

homo-dimer

Ligands

3 x SO4: SULFATE ION(Non-functional Binders)

SO4.1: 4 residues within 4Å: Chain A: F.7, T.8, R.9 Chain B: H.112 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:T.8, A:T.8, A:T.8, A:R.9 Salt bridges: A:R.9, B:H.112 SO4.6: 5 residues within 4Å: Chain A: H.112 Chain B: Q.6, F.7, T.8, R.9 7 PLIP interactions: 5 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:T.8, B:T.8 Water bridges: B:R.9, B:R.9, A:H.112 Salt bridges: B:R.9, A:H.112 SO4.7: 6 residues within 4Å: Chain B: T.28, D.29, V.30, V.31, R.40, S.66 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.28, B:V.30 Salt bridges: B:R.40

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 10 residues within 4Å: Chain A: L.27, D.29, H.42, K.43, T.44 Chain B: L.27, D.29, H.42, K.43, T.44 8 PLIP interactions: 4 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:D.29, B:K.43, B:T.44, B:T.44, A:K.43, A:T.44, A:T.44, A:T.44

2 x YJJ: N-[5-chloro-2-(morpholin-4-yl)pyridin-4-yl]-2-[5-(3-cyano-4-hydroxy-5-methylphenyl)-3-methyl-4-oxo-3,4-dihydro-7H-pyrrolo[2,3-d]pyrimidin-7-yl]acetamide(Non-covalent)

YJJ.3: 18 residues within 4Å: Chain A: M.47, A.48, C.49, S.50, G.51, Y.54, F.85, Q.109, M.110, E.111, H.112, V.113 Chain B: H.10, D.13, V.14, N.17, R.20, L.21 9 PLIP interactions: 4 interactions with chain B, 5 interactions with chain A Hydrophobic interactions: B:D.13, B:V.14 Hydrogen bonds: B:H.10, B:N.17, A:M.47, A:E.111, A:H.112, A:V.113 pi-Stacking: A:Y.54 YJJ.5: 19 residues within 4Å: Chain A: H.10, D.13, V.14, N.17, R.20, L.21, R.24 Chain B: M.47, A.48, C.49, S.50, G.51, Y.54, F.85, Q.109, M.110, E.111, H.112, V.113 12 PLIP interactions: 6 interactions with chain A, 6 interactions with chain B Hydrophobic interactions: A:D.13, A:V.14 Hydrogen bonds: A:H.10, A:N.17, A:R.20, B:M.47, B:Y.54, B:E.111, B:H.112, B:V.113 Water bridges: A:R.24 pi-Stacking: B:Y.54

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.4: 4 residues within 4Å: Chain A: R.63 Chain B: D.25, I.26, L.27 Ligand excluded by PLIP CL.8: 2 residues within 4Å: Chain B: I.56, K.62 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kuntz, D.A. et al., Crystal structure of the BCL6 BTB domain in complex with OICR-10256. To Be Published

Release Date

2022-03-16

Peptides

B-cell lymphoma 6 protein: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

B-cell lymphoma 6 protein

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