SMTL ID : 5h7h.1

Crystal structure of the BCL6 BTB domain in complex with F1324(10-13)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

homo-dimer

Ligands

4 x ACE- TRP- ARG- VAL- PRO: F1324 peptide residues 10-13(Non-covalent)

ACE-TRP-ARG-VAL-PRO.1: 13 residues within 4Å: Chain A: D.29, N.33, R.36, L.37, R.40 Chain B: M.63, A.64, C.65, S.66, G.67, Y.70, H.128 Ligands: EDO.3 14 PLIP interactions: 9 interactions with chain A, 5 interactions with chain B Hydrophobic interactions: A:N.33, A:R.36, A:L.37, B:Y.70, B:Y.70, B:Y.70, B:H.128 Hydrogen bonds: A:N.33, A:N.33, B:H.128 Water bridges: A:D.29 Salt bridges: A:D.29, A:R.36, A:R.40 ACE-TRP-ARG-VAL-PRO.2: 5 residues within 4Å: Chain A: Q.54, L.81, V.83, I.84, N.85 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:L.81, A:V.83 Hydrogen bonds: A:N.85 Water bridges: A:S.82, A:V.83 ACE-TRP-ARG-VAL-PRO.4: 13 residues within 4Å: Chain A: M.63, A.64, C.65, S.66, G.67, Y.70, H.128 Chain B: D.29, N.33, R.36, L.37, R.40 Ligands: EDO.6 13 PLIP interactions: 9 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:N.33, B:R.36, B:L.37, A:Y.70, A:Y.70, A:Y.70, A:H.128 Hydrogen bonds: B:N.33, B:N.33 Water bridges: B:D.29 Salt bridges: B:D.29, B:R.36, B:R.40 ACE-TRP-ARG-VAL-PRO.5: 5 residues within 4Å: Chain B: Q.54, L.81, V.83, I.84, N.85 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:L.81, B:V.83 Hydrogen bonds: B:N.85 Water bridges: B:S.82, B:V.83

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

EDO.3: 7 residues within 4Å: Chain A: H.26, D.29 Chain B: A.64, H.128 Ligands: ACE-TRP-ARG-VAL-PRO.1, ACE-TRP-ARG-VAL-PRO.1, ACE-TRP-ARG-VAL-PRO.1 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:H.128 EDO.6: 7 residues within 4Å: Chain A: A.64, H.128 Chain B: H.26, D.29 Ligands: ACE-TRP-ARG-VAL-PRO.4, ACE-TRP-ARG-VAL-PRO.4, ACE-TRP-ARG-VAL-PRO.4 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:H.26, B:D.29, A:H.128

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sakamoto, K. et al., Discovery of high-affinity BCL6-binding peptide and its structure-activity relationship. Biochem. Biophys. Res. Commun. (2017)

Release Date

2016-12-07

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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