SMTL ID : 8f0w.1

Tudor Domain of Tumor suppressor p53BP1 with MFP-5956

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.52 Å

Oligo State

homo-dimer

Ligands

2 x X9N: 1-[4-(4-ethylpiperazin-1-yl)-3-fluorophenyl]butan-1-one(Non-covalent)

X9N.1: 14 residues within 4Å: Chain A: W.14, N.17, Y.21, F.38, D.40, Y.42 Chain B: Y.19, Y.21, L.66, Y.71, F.72, I.106 Ligands: X9N.20, UNX.37 11 PLIP interactions: 6 interactions with chain A, 5 interactions with chain B Hydrophobic interactions: A:W.14, A:Y.21, A:F.38, B:Y.19, B:F.72, B:F.72, B:F.72 Salt bridges: A:D.40 pi-Cation interactions: A:W.14 Halogen bonds: A:Y.21 Hydrogen bonds: B:Y.21 X9N.20: 12 residues within 4Å: Chain A: N.17, Y.19, Y.21, L.66, F.72 Chain B: W.14, N.17, Y.21, F.38, D.40, Y.42 Ligands: X9N.1 11 PLIP interactions: 6 interactions with chain A, 5 interactions with chain B Hydrophobic interactions: A:Y.19, A:Y.19, A:F.72, A:F.72, A:F.72, B:Y.21, B:F.38 Hydrogen bonds: A:N.17, B:Y.71 Salt bridges: B:D.40 pi-Cation interactions: B:W.14

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

UNX.2: 2 residues within 4Å: Chain A: S.4, F.5 Ligand excluded by PLIP UNX.3: 3 residues within 4Å: Chain A: C.44, D.45 Chain B: E.68 Ligand excluded by PLIP UNX.4: 3 residues within 4Å: Chain A: K.82, S.84, G.85 Ligand excluded by PLIP UNX.5: 3 residues within 4Å: Chain A: E.86, L.87, R.102 Ligand excluded by PLIP UNX.6: 2 residues within 4Å: Chain A: S.90, R.97 Ligand excluded by PLIP UNX.7: 3 residues within 4Å: Chain A: Y.100, K.101, A.104 Ligand excluded by PLIP UNX.8: 3 residues within 4Å: Chain A: P.58, L.59, H.80 Ligand excluded by PLIP UNX.9: 1 residues within 4Å: Chain A: P.56 Ligand excluded by PLIP UNX.10: 2 residues within 4Å: Chain A: L.8, R.9 Ligand excluded by PLIP UNX.11: 3 residues within 4Å: Chain A: E.68 Chain B: C.44, D.45 Ligand excluded by PLIP UNX.12: 3 residues within 4Å: Chain A: K.49, P.123 Ligands: UNX.13 Ligand excluded by PLIP UNX.13: 5 residues within 4Å: Chain A: G.122, P.123, Y.124, E.125 Ligands: UNX.12 Ligand excluded by PLIP UNX.14: 3 residues within 4Å: Chain A: K.101, R.102, M.103 Ligand excluded by PLIP UNX.15: 2 residues within 4Å: Chain A: K.13, L.109 Ligand excluded by PLIP UNX.16: 3 residues within 4Å: Chain A: S.73, A.74, K.93 Ligand excluded by PLIP UNX.17: 2 residues within 4Å: Chain A: Q.96, R.97 Ligand excluded by PLIP UNX.18: 2 residues within 4Å: Chain A: E.70, Y.71 Ligand excluded by PLIP UNX.19: 2 residues within 4Å: Chain A: K.98, W.99 Ligand excluded by PLIP UNX.21: 4 residues within 4Å: Chain B: K.82, E.83, S.84, G.85 Ligand excluded by PLIP UNX.22: 4 residues within 4Å: Chain A: Y.71 Chain B: W.14, S.16, N.17 Ligand excluded by PLIP UNX.23: 3 residues within 4Å: Chain B: E.86, L.87, R.102 Ligand excluded by PLIP UNX.24: 2 residues within 4Å: Chain B: S.90, R.97 Ligand excluded by PLIP UNX.25: 2 residues within 4Å: Chain B: S.67, E.68 Ligand excluded by PLIP UNX.26: 2 residues within 4Å: Chain B: R.102, M.103 Ligand excluded by PLIP UNX.27: 4 residues within 4Å: Chain B: G.32, L.47, G.48, K.49 Ligand excluded by PLIP UNX.28: 2 residues within 4Å: Chain B: R.9, K.24 Ligand excluded by PLIP UNX.29: 1 residues within 4Å: Chain B: Q.118 Ligand excluded by PLIP UNX.30: 2 residues within 4Å: Chain B: G.75, V.76 Ligand excluded by PLIP UNX.31: 3 residues within 4Å: Chain B: S.108, E.110, Q.111 Ligand excluded by PLIP UNX.32: 2 residues within 4Å: Chain B: L.8, R.9 Ligand excluded by PLIP UNX.33: 1 residues within 4Å: Chain B: N.113 Ligand excluded by PLIP UNX.34: 1 residues within 4Å: Chain B: K.49 Ligand excluded by PLIP UNX.35: 2 residues within 4Å: Chain B: K.13, G.18 Ligand excluded by PLIP UNX.36: 2 residues within 4Å: Chain B: K.98, W.99 Ligand excluded by PLIP UNX.37: 2 residues within 4Å: Chain B: N.17 Ligands: X9N.1 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

The, J. et al., Tudor Domain of Tumor suppressor p53BP1 with MFP-5956. to be published

Release Date

2023-01-18

Peptides

TP53-binding protein 1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

TP53-binding protein 1

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