SMTL ID : 8uqa.1

Crystal structure of RNF168 (RING)-UbcH5c fused to H2A-H2B via a 12-residue linker

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.05 Å

Oligo State

monomer

Ligands

3 x NA: SODIUM ION(Non-functional Binders)

NA.1: 3 residues within 4Å: Chain A: E.23, I.24, V.26 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:I.24, A:V.26 NA.2: 1 residues within 4Å: Chain A: E.15 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.15 NA.9: 3 residues within 4Å: Chain A: S.254, G.255, N.380 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.254, A:N.380 Water bridges: A:Q.136, A:G.255

2 x ZN: ZINC ION(Non-covalent)

ZN.3: 4 residues within 4Å: Chain A: C.33, H.35, C.53, C.56 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.33, A:H.35, A:C.53, A:C.56 ZN.4: 4 residues within 4Å: Chain A: C.18, C.21, C.38, C.41 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.18, A:C.21, A:C.38, A:C.41

4 x CL: CHLORIDE ION(Non-functional Binders)

CL.5: 6 residues within 4Å: Chain A: T.319, S.320, G.386, A.387, G.388, A.389 Ligand excluded by PLIP CL.6: 4 residues within 4Å: Chain A: N.415, K.417, R.423, H.424 Ligand excluded by PLIP CL.7: 3 residues within 4Å: Chain A: R.377, R.384, V.385 Ligand excluded by PLIP CL.8: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hu, Q. et al., Mechanisms of RNF168 nucleosome recognition and ubiquitylation. Mol.Cell (2024)

Release Date

2024-01-17

Peptides

E3 ubiquitin-protein ligase RNF168,Ubiquitin-conjugating enzyme E2 D3,Histone H2B type 2-E,Histone H2A type 1-B/E: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
K

E3 ubiquitin-protein ligase RNF168,Ubiquitin-conjugating enzyme E2 D3,Histone H2B type 2-E,Histone H2A type 1-B/E