SMTL ID : 4x3k.1

Crystal structure of chromobox homolog 7 (CBX7) chromodomain with H3K27me3 peptide

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.45 Å

Oligo State

homo-dimer

Ligands

2 x LYS- ALA- ALA- ARG- M3L- SER- ALA: H3K27me3 peptide(Non-covalent)

LYS-ALA-ALA-ARG-M3L-SER-ALA.1: 17 residues within 4Å: Chain A: H.3, E.6, Q.7, V.8, F.9, A.10, V.11, W.30, W.33, Y.37, E.41, P.42, H.45, L.47, D.48, R.50, L.51 27 PLIP interactions: 27 interactions with chain A Hydrophobic interactions: A:V.8, A:V.11, A:W.30, A:W.30, A:H.45, A:L.47, A:L.51 Hydrogen bonds: A:E.6, A:Q.7, A:F.9, A:F.9, A:V.11, A:E.41, A:H.45, A:H.45, A:L.47, A:D.48 Water bridges: A:E.6, A:E.6, A:V.11, A:T.39, A:W.40, A:D.48 pi-Cation interactions: A:F.9, A:W.30, A:W.33, A:W.33 LYS-ALA-ALA-ARG-M3L-SER-ALA.2: 14 residues within 4Å: Chain B: H.3, E.6, Q.7, V.8, F.9, A.10, V.11, W.30, W.33, Y.37, E.41, H.45, L.47, D.48 24 PLIP interactions: 24 interactions with chain B Hydrophobic interactions: B:V.8, B:F.9, B:V.11, B:W.30, B:W.30, B:H.45 Hydrogen bonds: B:Q.7, B:F.9, B:F.9, B:V.11, B:E.41, B:H.45, B:L.47, B:D.48, B:R.50 Water bridges: B:H.3, B:H.3, B:E.6, B:Q.7, B:D.48 pi-Cation interactions: B:F.9, B:W.30, B:W.33, B:W.33

2 x NI: NICKEL (II) ION(Non-covalent)

NI.3: 3 residues within 4Å: Chain A: H.3, E.6, H.45 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.3, A:E.6, A:H.45 NI.4: 3 residues within 4Å: Chain B: H.3, E.6, H.45 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:H.3, B:E.6, B:E.6, B:H.45

1 x K: POTASSIUM ION(Non-covalent)

K.5: 4 residues within 4Å: Chain B: K.17, E.56, E.59, E.60 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:E.56, B:E.56, B:E.59, B:E.60

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ren, C. et al., Small-Molecule Modulators of Methyl-Lysine Binding for the CBX7 Chromodomain. Chem.Biol. (2015)

Release Date

2015-03-04

Peptides

Chromobox protein homolog 7: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Chromobox protein homolog 7

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