SMTL ID : 6a57.1

Structure of histone demethylase REF6 complexed with DNA

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

homo-dimer

Ligands

8 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: C.25, M.27, C.30, H.43, H.60 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.25, A:C.30, A:H.43, A:H.60 ZN.2: 4 residues within 4Å: Chain A: C.48, C.53, H.66, H.70 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.48, A:C.53, A:H.66, A:H.70 ZN.3: 4 residues within 4Å: Chain A: C.78, C.83, H.96, H.100 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.78, A:C.83, A:H.96, A:H.100 ZN.4: 4 residues within 4Å: Chain A: C.108, C.113, H.126, H.132 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.108, A:C.113, A:H.126, A:H.132 ZN.7: 5 residues within 4Å: Chain D: C.25, M.27, C.30, H.43, H.60 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:C.25, D:C.30, D:H.43, D:H.60 ZN.8: 4 residues within 4Å: Chain D: C.48, C.53, H.66, H.70 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:C.48, D:C.53, D:H.66, D:H.70 ZN.9: 4 residues within 4Å: Chain D: C.78, C.83, H.96, H.100 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:C.78, D:C.83, D:H.96, D:H.100 ZN.10: 4 residues within 4Å: Chain D: C.108, C.113, H.126, H.132 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:C.108, D:C.113, D:H.126, D:H.132

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 4 residues within 4Å: Chain C: A.12, G.13 Chain D: H.70, D.72 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:D.72 Water bridges: D:D.72 GOL.6: 2 residues within 4Å: Chain A: R.98 Chain C: C.9 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.98, A:Y.106, A:Y.106 GOL.11: 4 residues within 4Å: Chain A: H.70, D.72 Chain F: A.12, G.13 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.72 GOL.12: 2 residues within 4Å: Chain D: R.98 Chain F: C.9 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:R.98, D:Y.106

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tian, Z. et al., Crystal structures of REF6 and its complex with DNA reveal diverse recognition mechanisms. Cell Discov (2020)

Release Date

2019-06-26

Peptides

Lysine-specific demethylase REF6: AD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

D
A

Lysine-specific demethylase REF6

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