SMTL ID : 9ckj.3 (2 other biounits)

Co-crystal structure of 53BP1 tandem Tudor domains in complex with UNC9512

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.25 Å

Oligo State

homo-dimer

Ligands

2 x 01: (3S)-1-[4-(4-methylpiperazin-1-yl)pyridine-2-carbonyl]-N-[(3M)-3-(3-oxo-2,3-dihydro-1H-isoindol-5-yl)phenyl]piperidine-3-carboxamide

01.1: 19 residues within 4Å: Chain A: Y.18, Y.20, S.21, F.37, D.38, D.39, L.65, F.71, M.102, I.105 Chain B: W.13, N.16, Y.20, F.37, D.39, Y.41, E.69, F.71 Ligands: 01.2 16 PLIP interactions: 13 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:Y.20, A:Y.20, A:D.39, A:L.65, A:F.71, A:F.71, A:I.105, A:I.105, B:F.71 Hydrogen bonds: A:Y.18, A:Y.20, A:S.21, A:D.38, A:D.39 Salt bridges: B:D.39 pi-Cation interactions: B:W.13 01.2: 18 residues within 4Å: Chain A: W.13, Y.20, F.37, D.39, Y.41, E.69, F.71 Chain B: Y.18, Y.20, S.21, F.37, D.38, D.39, L.65, F.71, M.102, I.105 Ligands: 01.1 15 PLIP interactions: 11 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:Y.20, B:D.39, B:L.65, B:F.71, B:F.71, B:I.105, B:I.105, A:F.71 Hydrogen bonds: B:Y.20, B:S.21, B:D.38, B:D.39 Salt bridges: A:D.39 pi-Cation interactions: A:W.13, A:W.13

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

UNX.3: 2 residues within 4Å: Chain B: G.119, G.121 No protein-ligand interaction detected (PLIP) UNX.4: 1 residues within 4Å: Chain B: E.116 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zeng, H. et al., Co-crystal structure of 53BP1 tandem Tudor domains in complex with UNC9512. To be published

Release Date

2024-10-30

Peptides

TP53-binding protein 1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
E

B
F

TP53-binding protein 1

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