SMTL ID : 8uq9.1 (1 other biounit)

Crystal structure of RNF168 (RING)-UbcH5c fused to H2A-H2B via a 4-residue linker

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

monomer

Ligands

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

CL.1: 4 residues within 4Å: Chain A: Y.86, P.87, R.88, E.89 Ligand excluded by PLIP CL.2: 5 residues within 4Å: Chain A: A.4, L.5, I.81, K.84, H.85 Ligand excluded by PLIP CL.3: 4 residues within 4Å: Chain A: K.39, N.71, S.72, L.73 Ligand excluded by PLIP CL.4: 2 residues within 4Å: Chain A: E.27, W.79 Ligand excluded by PLIP CL.5: 2 residues within 4Å: Chain A: S.61, S.62 Ligand excluded by PLIP CL.6: 2 residues within 4Å: Chain A: P.6, K.7 Ligand excluded by PLIP CL.12: 3 residues within 4Å: Chain A: V.222, P.223, E.224 Ligand excluded by PLIP CL.13: 3 residues within 4Å: Chain A: P.146, N.237, R.241 Ligand excluded by PLIP CL.14: 2 residues within 4Å: Chain A: N.181, S.182 Ligand excluded by PLIP CL.15: 2 residues within 4Å: Chain A: K.168, S.185 Ligand excluded by PLIP CL.16: 6 residues within 4Å: Chain A: T.311, S.312, G.378, A.379, G.380, A.381 Ligand excluded by PLIP CL.17: 2 residues within 4Å: Chain A: R.363, R.366 Ligand excluded by PLIP CL.18: 1 residues within 4Å: Chain A: R.363 Ligand excluded by PLIP CL.19: 2 residues within 4Å: Chain A: R.366, R.369 Ligand excluded by PLIP CL.20: 2 residues within 4Å: Chain A: T.350, R.351 Ligand excluded by PLIP CL.21: 1 residues within 4Å: Chain A: R.313 Ligand excluded by PLIP CL.22: 3 residues within 4Å: Chain A: Q.316, T.317, R.320 Ligand excluded by PLIP

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 2 residues within 4Å: Chain A: W.63, H.67 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.67 GOL.8: 4 residues within 4Å: Chain A: P.11, E.15, L.78 Ligands: GOL.9 1 PLIP interactions: 1 interactions with chain A Water bridges: A:T.36 GOL.9: 7 residues within 4Å: Chain A: G.19, N.34, H.35, T.36, F.55, A.198 Ligands: GOL.8 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.34, A:T.36 Water bridges: A:G.19, A:T.36

2 x ZN: ZINC ION(Non-covalent)

ZN.10: 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.11: 5 residues within 4Å: Chain A: C.18, C.21, C.38, C.41, S.101 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.18, A:C.21, A:C.38, A:C.41

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

NA.23: 2 residues within 4Å: Chain A: M.140, Y.261 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.261

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
A

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

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