SMTL ID : 6v41.1

crystal structure of CDY1 chromodomain bound to H3K9me3

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

hetero-1-1-mer

Ligands

20 x UNX: UNKNOWN ATOM OR ION(Non-functional Binders)

UNX.1: 2 residues within 4Å: Chain A: D.35 Ligands: UNX.7 Ligand excluded by PLIP UNX.2: 2 residues within 4Å: Chain A: K.29, G.30 Ligand excluded by PLIP UNX.3: 3 residues within 4Å: Chain A: N.19, G.20, N.21 Ligand excluded by PLIP UNX.4: 8 residues within 4Å: Chain A: D.17, N.21, T.22, Q.23, P.40, E.41, Q.42 Ligands: UNX.9 Ligand excluded by PLIP UNX.5: 3 residues within 4Å: Chain A: D.32, K.33, Q.34 Ligand excluded by PLIP UNX.6: 4 residues within 4Å: Chain A: Q.23, W.38, E.39, P.40 Ligand excluded by PLIP UNX.7: 4 residues within 4Å: Chain A: D.35, T.37 Chain B: K.9 Ligands: UNX.1 Ligand excluded by PLIP UNX.8: 2 residues within 4Å: Chain A: K.29, G.30 Ligand excluded by PLIP UNX.9: 4 residues within 4Å: Chain A: N.21, E.41, Q.42 Ligands: UNX.4 Ligand excluded by PLIP UNX.10: 6 residues within 4Å: Chain A: R.27, W.28, Y.31, D.32, D.35, D.36 Ligand excluded by PLIP UNX.11: 2 residues within 4Å: Chain A: R.15, Q.16 Ligand excluded by PLIP UNX.12: 3 residues within 4Å: Chain A: E.9, K.29, G.30 Ligand excluded by PLIP UNX.13: 6 residues within 4Å: Chain A: A.10, I.11, C.50, F.54, R.57 Ligands: UNX.17 Ligand excluded by PLIP UNX.14: 4 residues within 4Å: Chain A: L.44, E.48, V.51 Ligands: UNX.15 Ligand excluded by PLIP UNX.15: 2 residues within 4Å: Chain A: V.51 Ligands: UNX.14 Ligand excluded by PLIP UNX.16: 1 residues within 4Å: Chain A: K.14 Ligand excluded by PLIP UNX.17: 4 residues within 4Å: Chain A: E.9, C.50, D.53 Ligands: UNX.13 Ligand excluded by PLIP UNX.18: 4 residues within 4Å: Chain A: M.45, N.46, C.47, E.48 Ligand excluded by PLIP UNX.19: 2 residues within 4Å: Chain B: S.10, T.11 Ligand excluded by PLIP UNX.20: 4 residues within 4Å: Chain A: E.7 Chain B: T.3, K.4, T.6 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dong, C. et al., Structural Basis for the Binding Selectivity of Human CDY Chromodomains. Cell Chem Biol (2020)

Release Date

2019-12-25

Peptides

Testis-specific chromodomain protein Y 1: A
Histone H3.1 Peptide: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
AAA

B
QQQ

Testis-specific chromodomain protein Y 1

Histone H3.1 Peptide

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