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

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-dimer

Ligands

2 x ALY: N(6)-ACETYLLYSINE(Non-covalent)

ALY.1: 7 residues within 4Å: Chain A: V.30, V.35, V.40, Y.43, Y.85, N.86, I.96 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:V.30, A:V.35, A:V.40, A:Y.85, A:I.96 Hydrogen bonds: A:N.86 ALY.13: 7 residues within 4Å: Chain B: V.30, V.35, V.40, Y.43, Y.85, N.86, I.96 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:V.30, B:V.35, B:V.40, B:Y.85, B:I.96 Hydrogen bonds: B:N.86

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

SO4.2: 3 residues within 4Å: Chain A: R.9, R.12, R.16 7 PLIP interactions: 7 interactions with chain A Water bridges: A:R.9, A:R.16, A:R.16, A:R.16 Salt bridges: A:R.9, A:R.12, A:R.16 SO4.3: 3 residues within 4Å: Chain A: K.64 Chain B: K.64 Ligands: SO4.15 11 PLIP interactions: 5 interactions with chain B, 6 interactions with chain A Water bridges: B:K.59, B:K.59, B:K.59, A:K.59, A:K.59, A:K.59, A:K.64 Salt bridges: B:K.59, B:K.64, A:K.59, A:K.64 SO4.14: 3 residues within 4Å: Chain B: R.9, R.12, R.16 7 PLIP interactions: 7 interactions with chain B Water bridges: B:R.9, B:R.16, B:R.16, B:R.16 Salt bridges: B:R.9, B:R.12, B:R.16 SO4.15: 3 residues within 4Å: Chain A: K.64 Chain B: K.64 Ligands: SO4.3 11 PLIP interactions: 6 interactions with chain B, 5 interactions with chain A Water bridges: B:K.59, B:K.59, B:K.59, B:K.64, A:K.59, A:K.59, A:K.59 Salt bridges: B:K.59, B:K.64, A:K.59, A:K.64

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

EDO.4: 5 residues within 4Å: Chain A: E.10, E.114, L.115, D.116, F.119 Ligand excluded by PLIP EDO.5: 4 residues within 4Å: Chain A: E.113, E.114, L.115, D.116 Ligand excluded by PLIP EDO.6: 5 residues within 4Å: Chain A: S.58, K.59, L.62 Chain B: K.48, P.50 Ligand excluded by PLIP EDO.7: 2 residues within 4Å: Chain A: D.105, Y.108 Ligand excluded by PLIP EDO.8: 6 residues within 4Å: Chain A: V.68, K.69, L.72, I.111, L.115, E.120 Ligand excluded by PLIP EDO.9: 1 residues within 4Å: Chain A: R.99 Ligand excluded by PLIP EDO.10: 1 residues within 4Å: Chain A: Q.3 Ligand excluded by PLIP EDO.11: 4 residues within 4Å: Chain A: F.8, H.63, L.66, R.130 Ligand excluded by PLIP EDO.12: 4 residues within 4Å: Chain A: V.30, K.33, P.34, V.35 Ligand excluded by PLIP EDO.16: 5 residues within 4Å: Chain B: E.10, E.114, L.115, D.116, F.119 Ligand excluded by PLIP EDO.17: 4 residues within 4Å: Chain B: E.113, E.114, L.115, D.116 Ligand excluded by PLIP EDO.18: 5 residues within 4Å: Chain A: K.48, P.50 Chain B: S.58, K.59, L.62 Ligand excluded by PLIP EDO.19: 2 residues within 4Å: Chain B: D.105, Y.108 Ligand excluded by PLIP EDO.20: 6 residues within 4Å: Chain B: V.68, K.69, L.72, I.111, L.115, E.120 Ligand excluded by PLIP EDO.21: 1 residues within 4Å: Chain B: R.99 Ligand excluded by PLIP EDO.22: 1 residues within 4Å: Chain B: Q.3 Ligand excluded by PLIP EDO.23: 4 residues within 4Å: Chain B: F.8, H.63, L.66, R.130 Ligand excluded by PLIP EDO.24: 4 residues within 4Å: Chain B: V.30, K.33, P.34, V.35 Ligand excluded by PLIP

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

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