SMTL ID : 7zwn.1

Crystal structure of human BCL6 BTB domain in complex with a WVIP peptide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.05 Å

Oligo State

homo-dimer

Ligands

4 x ALA- TRP- VAL- ILE- PRO- ALA: ALA-TRP-VAL-ILE-PRO-ALA(Non-covalent)

ALA-TRP-VAL-ILE-PRO-ALA.1: 13 residues within 4Å: Chain A: M.50, A.51, C.52, S.53, G.54, Y.57, H.115 Chain B: F.10, N.20, R.23, L.24, R.27 Ligands: EDO.13 11 PLIP interactions: 7 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:F.10, B:N.20, B:L.24, A:Y.57, A:Y.57, A:Y.57, A:H.115 Hydrogen bonds: B:N.20, B:N.20, B:R.23, B:R.27 ALA-TRP-VAL-ILE-PRO-ALA.2: 10 residues within 4Å: Chain A: C.7, I.8, Q.9, F.10, T.11 Chain B: F.88, R.93, L.94, H.115, T.119 13 PLIP interactions: 9 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:I.8, A:Q.9, A:F.10, A:F.10, B:F.88, B:L.94, B:L.94, B:T.119 Hydrogen bonds: A:Q.9, A:Q.9, A:T.11, A:T.11 Water bridges: A:R.12 ALA-TRP-VAL-ILE-PRO-ALA.9: 13 residues within 4Å: Chain A: F.10, N.20, R.23, L.24, R.27 Chain B: M.50, A.51, C.52, S.53, G.54, Y.57, H.115 Ligands: EDO.5 11 PLIP interactions: 7 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:F.10, A:N.20, A:L.24, B:Y.57, B:Y.57, B:Y.57, B:H.115 Hydrogen bonds: A:N.20, A:N.20, A:R.23, A:R.27 ALA-TRP-VAL-ILE-PRO-ALA.10: 10 residues within 4Å: Chain A: F.88, R.93, L.94, H.115, T.119 Chain B: C.7, I.8, Q.9, F.10, T.11 13 PLIP interactions: 4 interactions with chain A, 9 interactions with chain B Hydrophobic interactions: A:F.88, A:L.94, A:L.94, A:T.119, B:I.8, B:Q.9, B:F.10, B:F.10 Hydrogen bonds: B:Q.9, B:Q.9, B:T.11 Water bridges: B:T.11, B:R.12

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

EDO.3: 2 residues within 4Å: Chain A: I.71, N.72 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:V.70, A:N.72, A:N.72 EDO.4: 3 residues within 4Å: Chain A: D.62, Q.63, L.64 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.61, A:Q.63, A:L.64 EDO.5: 7 residues within 4Å: Chain A: F.10, H.13, D.16 Chain B: F.88, H.115 Ligands: ALA-TRP-VAL-ILE-PRO-ALA.9, ALA-TRP-VAL-ILE-PRO-ALA.9 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:D.16, B:H.115 EDO.6: 2 residues within 4Å: Chain A: E.80, G.99 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.80 EDO.11: 2 residues within 4Å: Chain B: I.71, N.72 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:V.70, B:N.72, B:N.72 EDO.12: 3 residues within 4Å: Chain B: D.62, Q.63, L.64 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.61, B:Q.63, B:L.64 EDO.13: 7 residues within 4Å: Chain A: F.88, H.115 Chain B: F.10, H.13, D.16 Ligands: ALA-TRP-VAL-ILE-PRO-ALA.1, ALA-TRP-VAL-ILE-PRO-ALA.1 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:H.13, B:D.16, B:D.16, A:H.115 EDO.14: 2 residues within 4Å: Chain B: E.80, G.99 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.80

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

DMS.7: 4 residues within 4Å: Chain A: D.87, T.91, R.93 Chain B: C.7 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:D.87 DMS.8: 3 residues within 4Å: Chain A: E.98, I.101, I.124 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.127 DMS.15: 4 residues within 4Å: Chain A: C.7 Chain B: D.87, T.91, R.93 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:D.87 DMS.16: 3 residues within 4Å: Chain B: E.98, I.101, I.124 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.98, B:S.127

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pierrat, O.A. et al., Discovering cell-active BCL6 inhibitors: effectively combining biochemical HTS with multiple biophysical techniques, X-ray crystallography and cell-based assays. Sci Rep (2022)

Release Date

2022-11-16

Peptides

B-cell lymphoma 6 protein: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

B-cell lymphoma 6 protein

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