SMTL ID : 5qxn.1

PanDDA analysis group deposition -- Crystal Structure of ATAD2 in complex with DF826

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.41 Å

Oligo State

monomer

Ligands

3 x RHG: (3aR,8S,9aS)-2-[(trifluoromethyl)sulfonyl]decahydro-3a,8-epoxypyrrolo[3,4-c]azocine(Non-covalent)

RHG.1: 8 residues within 4Å: Chain A: V.68, K.69, L.72, Y.108, I.111, L.115, E.120, E.124 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:K.69, A:E.120 RHG.2: 6 residues within 4Å: Chain A: A.23, I.24, T.32, L.53, S.54, I.57 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:I.57 Hydrogen bonds: A:T.32 Halogen bonds: A:A.23 RHG.3: 5 residues within 4Å: Chain A: V.46, E.84, Y.85, P.87, D.93 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:Y.85 Hydrogen bonds: A:D.93 Water bridges: A:D.88, A:D.88, A:D.93, A:D.93

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

SO4.4: 2 residues within 4Å: Chain A: R.89, R.94 3 PLIP interactions: 3 interactions with chain A Water bridges: A:R.89 Salt bridges: A:R.89, A:R.94 SO4.5: 2 residues within 4Å: Chain A: K.59, K.64 5 PLIP interactions: 5 interactions with chain A Water bridges: A:K.59, A:K.59, A:K.64 Salt bridges: A:K.59, A:K.64

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

EDO.6: 5 residues within 4Å: Chain A: E.10, 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.7: 4 residues within 4Å: Chain A: E.113, E.114, L.115, D.116 No protein-ligand interaction detected (PLIP) EDO.8: 4 residues within 4Å: Chain A: S.55, S.58, K.59, L.62 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Snee, M. et al., PanDDA analysis group deposition - Bromodomain of human ATAD2 fragment screening. To Be Published

Release Date

2020-04-08

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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