SMTL ID : 4qut.1

Structure of the bromodomain of human ATPase family AAA domain-containing protein 2 (ATAD2) complexed with Histone H4-K(ac)12

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

monomer

Ligands

1 x GLY- LEU- GLY- ALY- GLY: Histone H4(Non-covalent)

GLY-LEU-GLY-ALY-GLY.1: 10 residues within 4Å: Chain A: V.35, V.40, D.42, Y.43, Y.85, N.86, D.88, D.93, I.96 Ligands: EDO.4 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:V.35, A:I.96 Hydrogen bonds: A:N.86, A:D.88, A:D.93 Water bridges: A:Y.85

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

SO4.2: 3 residues within 4Å: Chain A: R.9, R.12, R.16 10 PLIP interactions: 10 interactions with chain A Water bridges: A:R.12, A:R.12, A:R.16, A:R.16, A:R.16, A:R.16, A:H.63 Salt bridges: A:R.9, A:R.12, A:R.16

11 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.3: 6 residues within 4Å: Chain A: E.10, F.14, E.114, L.115, D.116, F.119 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.10, A:E.114, A:D.116 EDO.4: 3 residues within 4Å: Chain A: Y.85 Ligands: GLY-LEU-GLY-ALY-GLY.1, GLY-LEU-GLY-ALY-GLY.1 No protein-ligand interaction detected (PLIP) EDO.5: 5 residues within 4Å: Chain A: I.111, K.112, L.115, E.117 Ligands: EDO.13 2 PLIP interactions: 2 interactions with chain A Water bridges: A:K.112, A:L.115 EDO.6: 4 residues within 4Å: Chain A: E.113, E.114, L.115, D.116 3 PLIP interactions: 3 interactions with chain A Water bridges: A:E.113, A:L.115, A:D.116 EDO.7: 2 residues within 4Å: Chain A: D.105, Y.108 No protein-ligand interaction detected (PLIP) EDO.8: 2 residues within 4Å: Chain A: R.94, R.97 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.94, A:R.97 Water bridges: A:R.97 EDO.9: 4 residues within 4Å: Chain A: S.55, S.58, K.59, L.62 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.55 EDO.10: 4 residues within 4Å: Chain A: K.59, K.64, D.70, R.73 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.59, A:K.59, A:D.70, A:R.73, A:R.73 EDO.11: 4 residues within 4Å: Chain A: K.26, R.29, R.99 Ligands: EDO.12 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.26, A:R.99 Water bridges: A:V.30 EDO.12: 2 residues within 4Å: Chain A: R.99 Ligands: EDO.11 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.99, A:R.99 EDO.13: 5 residues within 4Å: Chain A: L.72, I.111, L.115, E.120 Ligands: EDO.5 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Morozumi, Y. et al., Atad2 is a generalist facilitator of chromatin dynamics in embryonic stem cells. J Mol Cell Biol (2016)

Release Date

2014-07-30

Peptides

ATPase family AAA domain-containing protein 2: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

ATPase family AAA domain-containing protein 2

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