SMTL ID : 9j89.1 (1 other biounit)

zbp1 nucleic acid complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.58 Å

Oligo State

homo-dimer

Ligands

1 x DC- DA- DC- DG- DC- DA: DNA (5'-D(P*CP*AP*CP*GP*CP*A)-3')(Non-covalent)

DC-DA-DC-DG-DC-DA.1: 15 residues within 4Å: Chain A: L.25, K.36, R.37, N.40, Q.41, Y.44, A.58 Ligands: U-G-C-G-U-G.2, U-G-C-G-U-G.2, U-G-C-G-U-G.2, U-G-C-G-U-G.2, U-G-C-G-U-G.2, U-G-C-G-U-G.2, MG.3, MG.4 Protein-ligand interaction information (PLIP) not available

1 x U- G- C- G- U- G: RNA (5'-R(P*UP*GP*CP*GP*UP*G)-3')(Non-covalent)

U-G-C-G-U-G.2: 16 residues within 4Å: Chain B: L.25, K.36, R.37, N.40, Q.41, Y.44, P.57, A.58 Ligands: DC-DA-DC-DG-DC-DA.1, DC-DA-DC-DG-DC-DA.1, DC-DA-DC-DG-DC-DA.1, DC-DA-DC-DG-DC-DA.1, DC-DA-DC-DG-DC-DA.1, DC-DA-DC-DG-DC-DA.1, MG.7, MG.8 Protein-ligand interaction information (PLIP) not available

6 x MG: MAGNESIUM ION(Non-functional Binders)(Non-covalent)

MG.3: 1 residues within 4Å: Ligands: DC-DA-DC-DG-DC-DA.1 No protein-ligand interaction detected (PLIP) MG.4: 2 residues within 4Å: Ligands: DC-DA-DC-DG-DC-DA.1, DC-DA-DC-DG-DC-DA.1 No protein-ligand interaction detected (PLIP) MG.5: 1 residues within 4Å: Chain A: H.7 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.7, H2O.3 MG.6: 1 residues within 4Å: Chain B: H.7 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:H.7, H2O.5, H2O.5 MG.7: 1 residues within 4Å: Ligands: U-G-C-G-U-G.2 No protein-ligand interaction detected (PLIP) MG.8: 2 residues within 4Å: Ligands: U-G-C-G-U-G.2, U-G-C-G-U-G.2 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

He, J. et al., ZBP1 senses spliceosome stress through Z-RNA:DNA hybrid recognition. Mol.Cell (2025)

Release Date

2025-06-25

Peptides

Z-DNA-binding protein 1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

B
A

Z-DNA-binding protein 1

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