SMTL ID : 8ssu.1

ZnFs 3-11 of CCCTC-binding factor (CTCF) Complexed with 19mer DNA

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.89 Å

Oligo State

monomer

Ligands

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

EDO.1: 5 residues within 4Å: Chain A: Y.183, C.185, R.186, Q.187, H.190 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.183, A:Y.183, A:Q.187 EDO.10: 3 residues within 4Å: Chain B: T.13 Chain C: G.8, C.9 No protein-ligand interaction detected (PLIP)

8 x ZN: ZINC ION(Non-covalent)

ZN.2: 4 residues within 4Å: Chain A: C.5, C.8, H.21, H.26 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.5, A:C.8, A:H.21, A:H.26 ZN.3: 4 residues within 4Å: Chain A: C.34, C.37, H.50, H.54 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.34, A:C.37, A:H.50, A:H.54 ZN.4: 4 residues within 4Å: Chain A: C.62, C.65, H.78, H.82 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.62, A:C.65, A:H.78, A:H.82 ZN.5: 4 residues within 4Å: Chain A: C.90, C.93, H.106, H.111 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.90, A:C.93, A:H.106, A:H.111 ZN.6: 4 residues within 4Å: Chain A: C.120, C.123, H.136, H.141 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.120, A:C.123, A:H.136, A:H.141 ZN.7: 4 residues within 4Å: Chain A: C.150, C.153, H.166, H.170 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.150, A:C.153, A:H.166, A:H.170 ZN.8: 5 residues within 4Å: Chain A: C.178, Q.180, C.181, H.194, H.198 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.178, A:C.181, A:H.194, A:H.198 ZN.9: 4 residues within 4Å: Chain A: C.206, C.209, H.222, H.227 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.206, A:C.209, A:H.222, A:H.227

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yang, J. et al., Structures of CTCF-DNA complexes including all 11 zinc fingers. Nucleic Acids Res. (2023)

Release Date

2023-08-02

Peptides

Transcriptional repressor CTCF,LIM domain-binding protein 1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Transcriptional repressor CTCF,LIM domain-binding protein 1