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

Structure of the bromodomain of human ATPase family AAA domain-containing protein 2 (ATAD2) with bound MPD

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

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

SO4.1: 3 residues within 4Å: Chain A: R.9, R.12, R.16 7 PLIP interactions: 7 interactions with chain A Water bridges: A:R.12, A:R.16, A:R.16, A:R.16 Salt bridges: A:R.9, A:R.12, A:R.16 SO4.2: 1 residues within 4Å: Chain A: P.50 No protein-ligand interaction detected (PLIP) SO4.7: 3 residues within 4Å: Chain B: R.9, R.12, R.16 7 PLIP interactions: 7 interactions with chain B Water bridges: B:R.12, B:R.16, B:R.16, B:D.61 Salt bridges: B:R.9, B:R.12, B:R.16 SO4.8: 1 residues within 4Å: Chain B: P.50 No protein-ligand interaction detected (PLIP)

6 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.3: 6 residues within 4Å: Chain A: V.30, V.35, Y.43, Y.85, N.86, I.96 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:V.35, A:Y.85, A:I.96 Hydrogen bonds: A:N.86 Water bridges: A:N.81 MPD.4: 7 residues within 4Å: Chain A: E.10, F.14, E.114, L.115, D.116, F.119 Ligands: MPD.5 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:F.14, A:D.116, A:F.119, A:F.119 Hydrogen bonds: A:E.10, A:D.116 MPD.5: 7 residues within 4Å: Chain A: K.112, E.113, E.114, L.115, D.116 Chain B: H.20 Ligands: MPD.4 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:D.116 Water bridges: A:D.116 MPD.9: 6 residues within 4Å: Chain B: V.30, V.35, Y.43, Y.85, N.86, I.96 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:V.35, B:Y.85, B:I.96 Hydrogen bonds: B:N.86 Water bridges: B:N.81 MPD.10: 7 residues within 4Å: Chain B: E.10, F.14, E.114, L.115, D.116, F.119 Ligands: MPD.11 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:F.14, B:D.116, B:F.119, B:F.119 Hydrogen bonds: B:E.10, B:E.10, B:D.116 MPD.11: 7 residues within 4Å: Chain A: H.20 Chain B: K.112, E.113, E.114, L.115, D.116 Ligands: MPD.10 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:D.116 Water bridges: B:D.116, B:D.116

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 1 residues within 4Å: Chain A: L.115 No protein-ligand interaction detected (PLIP) GOL.12: 1 residues within 4Å: Chain B: L.115 No protein-ligand interaction detected (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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