SMTL ID : 6tbt.1

Crystal structure of the BCL6 BTB domain in complex with an Apt48 peptide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.63 Å

Oligo State

hetero-2-2-mer

Ligands

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

CL.1: 4 residues within 4Å: Chain A: M.111, E.112, H.113, V.114 Ligand excluded by PLIP CL.2: 3 residues within 4Å: Chain A: Q.61, R.64 Chain B: L.28 Ligand excluded by PLIP CL.3: 3 residues within 4Å: Chain A: V.35, S.36, R.37 Ligand excluded by PLIP CL.4: 3 residues within 4Å: Chain A: R.95, E.96, G.97 Ligand excluded by PLIP CL.5: 4 residues within 4Å: Chain B: M.111, E.112, H.113, V.114 Ligand excluded by PLIP

2 x MG: MAGNESIUM ION(Non-covalent)

MG.6: 2 residues within 4Å: Chain B: D.30, S.67 No protein-ligand interaction detected (PLIP) MG.7: 3 residues within 4Å: Chain B: G.97, N.98, A.101 No protein-ligand interaction detected (PLIP)

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.8: 9 residues within 4Å: Chain A: L.28, D.30, H.43, T.45 Chain B: L.28, D.30, H.43, K.44, T.45 9 PLIP interactions: 4 interactions with chain A, 5 interactions with chain B Hydrogen bonds: A:L.28, B:D.30, B:K.44, B:T.45, B:T.45 Water bridges: A:K.44, A:T.45, A:T.45, B:T.45

1 x NA: SODIUM ION(Non-functional Binders)

NA.9: 2 residues within 4Å: Chain B: N.65, S.67 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.67

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zacharchenko, T. et al., Structural basis of Apt48 inhibition of the BCL6 BTB domain. Structure (2021)

Release Date

2021-10-13

Peptides

B-cell lymphoma 6 protein: AB
Apt48 peptide: CD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

B-cell lymphoma 6 protein

Apt48 peptide

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