SMTL ID : 4qsx.1

Structure of the bromodomain of human ATPase family AAA domain-containing protein 2 (ATAD2) in complex with 3'-deoxy thymidine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.93 Å

Oligo State

monomer

Ligands

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

SO4.1: 2 residues within 4Å: Chain A: R.89, R.94 4 PLIP interactions: 4 interactions with chain A Water bridges: A:R.89, A:R.89 Salt bridges: A:R.89, A:R.94

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

EDO.2: 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.3: 4 residues within 4Å: Chain A: E.113, E.114, L.115, D.116 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.114 Water bridges: A:D.116 EDO.4: 1 residues within 4Å: Chain A: K.64 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.64 Water bridges: A:K.64 EDO.5: 5 residues within 4Å: Chain A: K.69, L.72, I.111, L.115, E.120 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.120 EDO.6: 3 residues within 4Å: Chain A: R.104, D.105, Y.108 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.105

1 x 38S: 1-[(2R,5S)-5-(hydroxymethyl)tetrahydrofuran-2-yl]-5-methylpyrimidine-2,4(1H,3H)-dione(Non-covalent)

38S.7: 8 residues within 4Å: Chain A: V.30, V.35, E.39, V.40, Y.43, Y.85, N.86, I.96 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:V.35, A:V.40, A:I.96 Hydrogen bonds: A:N.86, A:N.86

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chaikuad, A. et al., Structure-based approaches towards identification of fragments for the low-druggability ATAD2 bromodomain. MedChemComm (2014)

Release Date

2014-07-23

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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