SMTL ID : 4mzf.1

Crystal structure of human Spindlin1 bound to histone H3(K4me3-R8me2a) peptide

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

monomer

Ligands

1 x ALA- ARG- THR- M3L- GLN- THR- ALA- DA2- LYS: Peptide from Histone H3.2(Non-covalent)

ALA-ARG-THR-M3L-GLN-THR-ALA-DA2-LYS.1: 22 residues within 4Å: Chain A: W.24, E.26, W.34, Y.53, G.55, F.56, D.57, Y.60, M.102, F.103, E.104, W.113, Y.132, D.135, Y.139, Y.141, Q.142, D.146, D.151, D.211, D.212, F.213 29 PLIP interactions: 29 interactions with chain A Hydrogen bonds: A:W.24, A:G.55, A:D.57, A:E.104, A:E.104, A:Q.142, A:Q.142, A:D.211, A:F.213 Water bridges: A:D.57, A:C.58, A:Y.60, A:Y.60, A:M.102, A:E.104, A:Q.142, A:Q.142, A:D.151, A:Y.216 Salt bridges: A:E.26, A:D.135, A:D.146 pi-Cation interactions: A:W.24, A:Y.60, A:F.103, A:W.113, A:W.113, A:Y.132, A:Y.139

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.2: 3 residues within 4Å: Chain A: W.113, R.114, K.134 Ligand excluded by PLIP CL.3: 4 residues within 4Å: Chain A: A.119, H.196, V.198, E.199 Ligand excluded by PLIP

1 x MG: MAGNESIUM ION(Non-functional Binders)

MG.4: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Su, X. et al., Molecular basis underlying histone H3 lysine-arginine methylation pattern readout by Spin/Ssty repeats of Spindlin1. Genes Dev. (2014)

Release Date

2014-03-26

Peptides

Spindlin-1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

Spindlin-1

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