SMTL ID : 4h75.1

Crystal structure of human Spindlin1 in complex with a histone H3K4(me3) peptide

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

monomer

Ligands

1 x ALA- ARG- THR- M3L- GLN- THR- ALA- ARG: Histone H3(Non-covalent)

ALA-ARG-THR-M3L-GLN-THR-ALA-ARG.1: 20 residues within 4Å: Chain A: G.69, F.70, D.71, C.72, Y.74, M.116, F.117, E.118, W.127, Y.146, D.149, V.151, Y.153, Y.155, Q.156, D.160, D.165, H.228 Ligands: SO4.4, SO4.6 26 PLIP interactions: 26 interactions with chain A Hydrophobic interactions: A:E.118 Hydrogen bonds: A:G.69, A:D.71, A:Y.74, A:E.118, A:E.118, A:E.118, A:Q.156, A:Q.156, A:D.165 Water bridges: A:D.71, A:C.72, A:M.116, A:Q.156, A:Q.156, A:Q.156, A:D.165 Salt bridges: A:D.149, A:D.160, A:H.228 pi-Cation interactions: A:F.117, A:W.127, A:W.127, A:Y.146, A:Y.153, A:H.228

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 7 residues within 4Å: Chain A: V.94, S.97, M.138, N.139, T.140, W.141, Q.156 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.97, A:N.139, A:T.140, A:T.140, A:Q.156

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

SO4.3: 3 residues within 4Å: Chain A: V.84, S.85, A.86 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:V.84, A:A.86 Water bridges: A:L.87 SO4.4: 5 residues within 4Å: Chain A: D.159, D.160, E.163 Ligands: ALA-ARG-THR-M3L-GLN-THR-ALA-ARG.1, ALA-ARG-THR-M3L-GLN-THR-ALA-ARG.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.163 SO4.6: 3 residues within 4Å: Ligands: ALA-ARG-THR-M3L-GLN-THR-ALA-ARG.1, ALA-ARG-THR-M3L-GLN-THR-ALA-ARG.1, ALA-ARG-THR-M3L-GLN-THR-ALA-ARG.1 No protein-ligand interaction detected (PLIP)

1 x NHE: 2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID(Non-covalent)

NHE.5: 6 residues within 4Å: Chain A: W.38, E.40, W.48, Y.67, Y.74, L.76 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:W.38, A:W.38, A:W.48, A:W.48, A:Y.67, A:Y.74, A:L.76 Hydrogen bonds: A:E.40 Water bridges: A:E.40

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yang, N. et al., Distinct mode of methylated lysine-4 of histone H3 recognition by tandem tudor-like domains of Spindlin1. Proc.Natl.Acad.Sci.USA (2012)

Release Date

2012-10-03

Peptides

Spindlin-1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Spindlin-1