SMTL ID : 6xzz.1

Crystal structure of the BCL6 BTB domain in complex with the NCoR1 BBD2 peptide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.39 Å

Oligo State

hetero-2-2-mer

Ligands

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

NA.1: 4 residues within 4Å: Chain A: R.21, L.22, R.25 Chain C: Y.55 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:Y.55 Water bridges: A:L.22 NA.2: 4 residues within 4Å: Chain A: T.59, D.60, Q.61 Ligands: NA.3 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.59, A:Q.61 NA.3: 3 residues within 4Å: Chain A: Q.61, L.62 Ligands: NA.2 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.61, A:L.62 NA.4: 3 residues within 4Å: Chain A: L.66, S.67, V.68 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.67, A:V.68 NA.5: 2 residues within 4Å: Chain A: I.82, N.98 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.98 Water bridges: A:G.97 NA.6: 3 residues within 4Å: Chain A: L.17, N.20, T.89 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.20 NA.7: 5 residues within 4Å: Chain A: S.36, P.73, E.74, I.75, P.77 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.36, A:E.74 NA.11: 4 residues within 4Å: Chain A: Y.55 Chain C: R.21, L.22, R.25 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:Y.55, A:Y.55 Water bridges: C:L.22 NA.12: 4 residues within 4Å: Chain C: T.59, D.60, Q.61 Ligands: NA.13 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:T.59, C:Q.61 NA.13: 3 residues within 4Å: Chain C: Q.61, L.62 Ligands: NA.12 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:Q.61, C:L.62 Water bridges: C:D.60, C:D.60 NA.14: 3 residues within 4Å: Chain C: L.66, S.67, V.68 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:S.67, C:V.68 NA.15: 2 residues within 4Å: Chain C: I.82, N.98 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:N.98 Water bridges: C:G.97 NA.16: 3 residues within 4Å: Chain C: L.17, N.20, T.89 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.20 NA.17: 5 residues within 4Å: Chain C: S.36, P.73, E.74, I.75, P.77 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:S.36, C:E.74

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

CL.8: 4 residues within 4Å: Chain A: M.111, E.112, H.113, V.114 Ligand excluded by PLIP CL.9: 4 residues within 4Å: Chain A: R.64 Chain C: D.26, I.27, L.28 Ligand excluded by PLIP CL.18: 4 residues within 4Å: Chain C: M.111, E.112, H.113, V.114 Ligand excluded by PLIP CL.19: 4 residues within 4Å: Chain A: D.26, I.27, L.28 Chain C: R.64 Ligand excluded by PLIP

2 x TFA: trifluoroacetic acid(Non-covalent)

TFA.10: 5 residues within 4Å: Chain B: L.11, Y.12, L.13 Chain C: K.120, F.121 3 PLIP interactions: 3 interactions with chain C Water bridges: C:K.120, C:K.120 Salt bridges: C:K.120 TFA.20: 5 residues within 4Å: Chain A: K.120, F.121 Chain D: L.11, Y.12, L.13 3 PLIP interactions: 3 interactions with chain A Water bridges: A:K.120, A:K.120 Salt bridges: A:K.120

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zacharchenko, T. et al., Functionalization of the BCL6 BTB domain into a noncovalent crystallization chaperone. Iucrj (2021)

Release Date

2020-12-02

Peptides

B-cell lymphoma 6 protein: AC
Nuclear receptor corepressor 1: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
A

B
B

D
B

B-cell lymphoma 6 protein

Nuclear receptor corepressor 1

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