SMTL ID : 4rg2.1

Tudor Domain of Tumor suppressor p53BP1 with small molecule ligand

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

homo-dimer

Ligands

1 x 3OO: 3-bromo-N-[3-(tert-butylamino)propyl]benzamide(Non-covalent)

3OO.1: 14 residues within 4Å: Chain A: W.14, Y.21, F.38, D.40, Y.42, L.66, M.103 Chain B: W.14, Y.21, D.40, Y.42, M.103 Ligands: UNX.4, UNX.12 13 PLIP interactions: 8 interactions with chain B, 5 interactions with chain A Hydrophobic interactions: B:W.14, B:W.14, B:Y.21, B:D.40, B:Y.42, A:F.38, A:Y.42, A:L.66 Hydrogen bonds: B:D.40, B:D.40, B:D.40, A:D.39, A:D.40

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

EDO.2: 5 residues within 4Å: Chain A: D.69, E.70, Y.71, F.72, S.73 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.69, A:Y.71, A:F.72, A:F.72 EDO.3: 1 residues within 4Å: Chain A: R.27 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.27 EDO.11: 6 residues within 4Å: Chain B: D.28, V.29, G.30, G.32, K.33, Y.34 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:V.29, B:G.30, B:G.32, B:K.33, B:K.33

12 x UNX: UNKNOWN ATOM OR ION(Non-functional Binders)

UNX.4: 3 residues within 4Å: Chain A: S.22, D.39 Ligands: 3OO.1 No protein-ligand interaction detected (PLIP) UNX.5: 3 residues within 4Å: Chain A: Y.71, F.72 Chain B: G.41 No protein-ligand interaction detected (PLIP) UNX.6: 2 residues within 4Å: Chain A: C.44, D.45 No protein-ligand interaction detected (PLIP) UNX.7: 2 residues within 4Å: Chain A: D.60, V.76 No protein-ligand interaction detected (PLIP) UNX.8: 3 residues within 4Å: Chain A: K.49, R.116, G.122 No protein-ligand interaction detected (PLIP) UNX.9: 3 residues within 4Å: Chain A: W.99, Y.100 Chain B: E.86 No protein-ligand interaction detected (PLIP) UNX.10: 3 residues within 4Å: Chain A: P.58, L.59, H.80 No protein-ligand interaction detected (PLIP) UNX.12: 4 residues within 4Å: Chain B: S.22, D.39, M.103 Ligands: 3OO.1 No protein-ligand interaction detected (PLIP) UNX.13: 3 residues within 4Å: Chain A: G.41 Chain B: Y.71, F.72 No protein-ligand interaction detected (PLIP) UNX.14: 4 residues within 4Å: Chain B: D.69, E.70, Y.71, F.72 No protein-ligand interaction detected (PLIP) UNX.15: 1 residues within 4Å: Chain B: W.99 No protein-ligand interaction detected (PLIP) UNX.16: 2 residues within 4Å: Chain A: M.103 Chain B: M.103 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Perfetti, M.T. et al., Identification of a fragment-like small molecule ligand for the methyl-lysine binding protein, 53BP1. ACS Chem. Biol. (2015)

Release Date

2014-10-15

Peptides

Tumor suppressor p53-binding protein 1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Tumor suppressor p53-binding protein 1

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