SMTL ID : 4qsv.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 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

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

EDO.2: 5 residues within 4Å: Chain A: E.5, F.8, R.12, H.63, L.66 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.5, A:R.12, A:R.12, A:H.63 Water bridges: A:E.5 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: 5 residues within 4Å: Chain A: K.69, L.72, R.73, D.76, Y.108 1 PLIP interactions: 1 interactions with chain A Water bridges: A:D.76 EDO.5: 4 residues within 4Å: Chain A: E.113, E.114, L.115, D.116 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:L.115 EDO.6: 4 residues within 4Å: Chain A: K.69, L.72, I.111, E.120 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.120 EDO.7: 5 residues within 4Å: Chain A: K.59, K.64, Y.65, D.70, D.74 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.59, A:D.70, A:D.74 Water bridges: A:R.73, A:R.73 EDO.8: 3 residues within 4Å: Chain A: R.104, D.105, Y.108 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.104, A:R.104 EDO.9: 3 residues within 4Å: Chain A: Q.121, E.124, E.128 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.121, A:E.124

1 x THM: THYMIDINE(Non-covalent)

THM.10: 8 residues within 4Å: Chain A: V.30, V.35, E.39, V.40, Y.43, Y.85, N.86, I.96 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:V.30, A:V.35, A:V.40, A:I.96 Hydrogen bonds: A:E.39, 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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