SMTL ID : 4qsu.2 (1 other biounit)

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-dimer

Ligands

4 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 SO4.2: 5 residues within 4Å: Chain A: K.59, K.64 Chain B: K.59, K.64 Ligands: SO4.12 9 PLIP interactions: 5 interactions with chain A, 4 interactions with chain B Water bridges: A:K.59, A:K.59, A:K.59, B:K.59, B:K.59 Salt bridges: A:K.59, A:K.64, B:K.59, B:K.64 SO4.11: 2 residues within 4Å: Chain B: R.89, R.94 4 PLIP interactions: 4 interactions with chain B Water bridges: B:R.89, B:R.89 Salt bridges: B:R.89, B:R.94 SO4.12: 5 residues within 4Å: Chain A: K.59, K.64 Chain B: K.59, K.64 Ligands: SO4.2 9 PLIP interactions: 4 interactions with chain A, 5 interactions with chain B Water bridges: A:K.59, A:K.59, B:K.59, B:K.59, B:K.59 Salt bridges: A:K.59, A:K.64, B:K.59, B:K.64

14 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 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.10, 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 Water bridges: A:D.116 EDO.5: 4 residues within 4Å: Chain A: C.79, C.101, R.104, D.105 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.104, A:D.105 EDO.6: 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 Water bridges: A:D.105 EDO.7: 3 residues within 4Å: Chain A: D.61, L.62, H.63 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.61 Water bridges: A:L.62 EDO.8: 3 residues within 4Å: Chain A: G.92, D.93 Ligands: TDR.10 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.93, A:D.93 EDO.9: 3 residues within 4Å: Chain A: D.105, T.106, A.109 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.106 EDO.13: 5 residues within 4Å: Chain B: E.10, E.114, L.115, D.116, F.119 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.10, B:E.114, B:D.116 EDO.14: 4 residues within 4Å: Chain B: E.113, E.114, L.115, D.116 No protein-ligand interaction detected (PLIP) EDO.15: 4 residues within 4Å: Chain B: C.79, C.101, R.104, D.105 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.104, B:D.105 EDO.16: 3 residues within 4Å: Chain B: R.104, D.105, Y.108 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.104, B:D.105 Water bridges: B:D.105 EDO.17: 3 residues within 4Å: Chain B: D.61, L.62, H.63 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.61 Water bridges: B:L.62 EDO.18: 3 residues within 4Å: Chain B: G.92, D.93 Ligands: TDR.20 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.93 EDO.19: 3 residues within 4Å: Chain B: D.105, T.106, A.109 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:T.106

2 x TDR: THYMINE(Non-covalent)

TDR.10: 7 residues within 4Å: Chain A: V.30, V.35, Y.43, Y.85, N.86, I.96 Ligands: EDO.8 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:V.30, A:V.35, A:I.96 Hydrogen bonds: A:N.86, A:N.86 TDR.20: 7 residues within 4Å: Chain B: V.30, V.35, Y.43, Y.85, N.86, I.96 Ligands: EDO.18 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:V.30, B:V.35, B:I.96 Hydrogen bonds: B:N.86, B: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: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

ATPase family AAA domain-containing protein 2

Related Entries With Identical Sequence