SMTL ID : 5qxm.1

PanDDA analysis group deposition -- Crystal Structure of ATAD2 in complex with DF789

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

monomer

Ligands

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

SO4.1: 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 SO4.2: 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

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

EDO.3: 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.4: 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.5: 4 residues within 4Å: Chain A: S.55, S.58, K.59, L.62 No protein-ligand interaction detected (PLIP) EDO.7: 4 residues within 4Å: Chain A: N.86, D.93, I.96 Ligands: RHJ.6 2 PLIP interactions: 2 interactions with chain A Water bridges: A:Y.85, A:D.93 EDO.8: 2 residues within 4Å: Chain A: V.30 Ligands: EDO.9 1 PLIP interactions: 1 interactions with chain A Water bridges: A:V.30 EDO.9: 5 residues within 4Å: Chain A: V.30, I.96, R.99 Ligands: RHJ.6, EDO.8 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.99

1 x RHJ: cyclobutyl[(3aS,4R,5R,7S,8aS)-4,5-dihydroxyhexahydro-1H-3a,7-epoxycyclohepta[c]pyrrol-2(3H)-yl]methanone(Non-covalent)

RHJ.6: 10 residues within 4Å: Chain A: V.30, F.31, V.35, V.40, Y.43, Y.85, N.86, I.96 Ligands: EDO.7, EDO.9 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:V.30, A:V.30, A:F.31, A:V.35, A:I.96 Hydrogen bonds: A:N.86 Water bridges: A:E.39

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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