SMTL ID : 6zbu.1

Crystal structure of an NCoR1BBD2-BCL6BTB chimera in complex with the NcoR1 BBD1 corepressor peptide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.46 Å

Oligo State

hetero-6-6-mer

Ligands

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

SO4.1: 3 residues within 4Å: Chain A: Y.66 Chain B: R.36 Chain C: P.16 Ligand excluded by PLIP SO4.2: 7 residues within 4Å: Chain A: H.124, D.127, T.128, K.131 Chain C: E.7, G.9, R.10 Ligand excluded by PLIP SO4.3: 3 residues within 4Å: Chain A: R.102, N.104 Chain B: Q.16 Ligand excluded by PLIP SO4.4: 4 residues within 4Å: Chain A: L.28, N.31, R.32 Chain D: R.17 Ligand excluded by PLIP SO4.6: 2 residues within 4Å: Chain B: R.21 Chain C: R.10 Ligand excluded by PLIP SO4.7: 3 residues within 4Å: Chain A: R.36 Chain B: Y.66 Chain D: P.16 Ligand excluded by PLIP SO4.8: 3 residues within 4Å: Chain A: Q.16 Chain B: R.102, N.104 Ligand excluded by PLIP SO4.9: 6 residues within 4Å: Chain A: S.101, R.102 Chain B: Q.18, F.19, T.20 Ligands: GOL.5 Ligand excluded by PLIP SO4.11: 3 residues within 4Å: Chain A: R.21 Chain D: R.10, E.14 Ligand excluded by PLIP SO4.13: 3 residues within 4Å: Chain E: Q.50, F.51, R.52 Ligand excluded by PLIP SO4.14: 3 residues within 4Å: Chain E: R.21 Chain L: R.10, E.14 Ligand excluded by PLIP SO4.15: 4 residues within 4Å: Chain E: R.75 Chain F: D.37, L.39, T.40 Ligand excluded by PLIP SO4.16: 3 residues within 4Å: Chain E: R.102, N.104 Chain F: Q.16 Ligand excluded by PLIP SO4.17: 6 residues within 4Å: Chain E: D.37, L.39, T.40 Chain F: Q.72, R.75 Chain H: N.76 Ligand excluded by PLIP SO4.18: 4 residues within 4Å: Chain E: H.124 Chain G: R.10, H.13, E.14 Ligand excluded by PLIP SO4.19: 2 residues within 4Å: Chain F: R.21 Chain G: R.10 Ligand excluded by PLIP SO4.20: 3 residues within 4Å: Chain E: Y.66 Chain F: R.36 Chain G: P.16 Ligand excluded by PLIP SO4.21: 3 residues within 4Å: Chain H: Q.50, F.51, R.52 Ligand excluded by PLIP SO4.22: 3 residues within 4Å: Chain H: R.21 Chain K: R.10, E.14 Ligand excluded by PLIP SO4.23: 3 residues within 4Å: Chain H: R.102, N.104 Chain I: Q.16 Ligand excluded by PLIP SO4.25: 6 residues within 4Å: Chain B: G.1 Chain E: N.76 Chain H: D.37, L.39 Chain I: Q.72, R.75 Ligand excluded by PLIP SO4.26: 3 residues within 4Å: Chain I: R.21 Chain J: R.10, E.14 Ligand excluded by PLIP SO4.27: 3 residues within 4Å: Chain H: Y.66 Chain I: R.36 Chain J: P.16 Ligand excluded by PLIP SO4.28: 1 residues within 4Å: Chain I: R.36 Ligand excluded by PLIP SO4.29: 3 residues within 4Å: Chain H: R.75 Chain I: L.39, T.40 Ligand excluded by PLIP SO4.30: 5 residues within 4Å: Chain H: H.124 Chain J: R.10, I.12, H.13, E.14 Ligand excluded by PLIP SO4.31: 4 residues within 4Å: Chain I: H.124 Chain K: R.10, H.13, E.14 Ligand excluded by PLIP SO4.32: 4 residues within 4Å: Chain F: H.124 Chain L: R.10, H.13, E.14 Ligand excluded by PLIP

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 8 residues within 4Å: Chain A: S.24, T.100, S.101 Chain B: F.19, T.20, H.22, A.23 Ligands: SO4.9 7 PLIP interactions: 4 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:S.24, A:T.100, A:S.101, A:S.101, B:H.22, B:A.23 Water bridges: B:S.24 GOL.10: 5 residues within 4Å: Chain A: H.124 Chain C: R.10, I.12, H.13, E.14 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:E.14, A:H.124 GOL.12: 4 residues within 4Å: Chain B: H.124 Chain D: R.10, H.13, E.14 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:E.14, D:E.14 GOL.24: 1 residues within 4Å: Chain H: R.52 4 PLIP interactions: 2 interactions with chain H, 2 interactions with chain B Hydrogen bonds: H:R.52, H:R.52 Water bridges: B:S.3, B:D.5

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

Nuclear receptor corepressor 1,B-cell lymphoma 6 protein: ABEFHI
Nuclear receptor corepressor 1: CDGJKL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

E
E

F
F

H
I

I
J

C
C

D
D

G
G

J
K

K
L

L
H

Nuclear receptor corepressor 1,B-cell lymphoma 6 protein

Nuclear receptor corepressor 1

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