SMTL ID : 8tx8.1 (1 other biounit)

Crystal Structure of RBBP4 bound to ZNF512B peptide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

hetero-1-1-mer

Ligands

3 x FMT: FORMIC ACID(Non-functional Binders)

FMT.1: 2 residues within 4Å: Chain A: R.194, V.236 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.194, A:R.194 FMT.6: 5 residues within 4Å: Chain A: E.95, N.97, N.142, H.143, G.185 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.97, A:H.143 FMT.10: 5 residues within 4Å: Chain A: L.65, R.149, F.341, S.398 Chain B: R.5 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:R.5, B:R.5, A:R.149

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

EDO.2: 2 residues within 4Å: Chain A: D.381, L.387 No protein-ligand interaction detected (PLIP) EDO.3: 3 residues within 4Å: Chain A: D.322, R.324, L.330 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.322, A:R.324 EDO.4: 4 residues within 4Å: Chain A: D.268, Q.270, A.294, E.295 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.295 Water bridges: A:D.268, A:E.295 EDO.5: 3 residues within 4Å: Chain A: D.315, T.317, E.334 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.315, A:E.334 EDO.7: 3 residues within 4Å: Chain A: K.316, K.337, D.338 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.316 Water bridges: A:K.316, A:D.338 EDO.8: 2 residues within 4Å: Chain A: E.426, N.427 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.426 EDO.9: 6 residues within 4Å: Chain A: S.335, K.337, D.359, R.361, N.363, I.389 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.336, A:D.359, A:N.363

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wunderlich, T.M. et al., ZNF512B binds RBBP4 via a variant NuRD interaction motif and aggregates chromatin in a NuRD complex-independent manner. Nucleic Acids Res. (2024)

Release Date

2024-11-06

Peptides

Histone-binding protein RBBP4: A
Zinc finger protein 512B: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
D

Histone-binding protein RBBP4

Zinc finger protein 512B

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