SMTL ID : 8uq9.2 (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

19 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: 3 residues within 4Å: Chain A: S.12, L.13, Y.86 Ligand excluded by PLIP CL.4: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.5: 4 residues within 4Å: Chain A: K.39, N.71, S.72, L.73 Ligand excluded by PLIP CL.6: 5 residues within 4Å: Chain A: C.21, G.102, S.103, K.106, R.107 Ligand excluded by PLIP CL.7: 2 residues within 4Å: Chain A: P.6, K.7 Ligand excluded by PLIP CL.8: 2 residues within 4Å: Chain A: W.63, H.67 Ligand excluded by PLIP CL.14: 3 residues within 4Å: Chain A: N.181, S.182, V.222 Ligand excluded by PLIP CL.15: 2 residues within 4Å: Chain A: H.134, H.157 Ligand excluded by PLIP CL.16: 3 residues within 4Å: Chain A: P.146, N.237, R.241 Ligand excluded by PLIP CL.17: 3 residues within 4Å: Chain A: Y.229, K.230, R.233 Ligand excluded by PLIP CL.18: 4 residues within 4Å: Chain A: S.124, Q.136, A.137, T.138 Ligand excluded by PLIP CL.20: 6 residues within 4Å: Chain A: M.140, G.149, S.257, Y.258, S.259, I.260 Ligand excluded by PLIP CL.21: 1 residues within 4Å: Chain A: R.313 Ligand excluded by PLIP CL.22: 2 residues within 4Å: Chain A: R.293, L.322 Ligand excluded by PLIP CL.25: 6 residues within 4Å: Chain A: T.311, S.312, G.378, A.379, G.380, A.381 Ligand excluded by PLIP CL.26: 2 residues within 4Å: Chain A: T.350, R.351 Ligand excluded by PLIP CL.27: 2 residues within 4Å: Chain A: R.366, R.369 Ligand excluded by PLIP

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

NA.9: 3 residues within 4Å: Chain A: S.61, S.62, R.65 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.61, A:R.65, A:R.65 Water bridges: A:S.61 NA.19: 2 residues within 4Å: Chain A: C.187, D.219 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.219 NA.23: 3 residues within 4Å: Chain A: R.320, L.321, L.323 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.320

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.10: 2 residues within 4Å: Chain A: E.15, L.78 No protein-ligand interaction detected (PLIP) GOL.11: 5 residues within 4Å: Chain A: G.19, H.35, T.36, F.55, A.198 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.19, A:N.34, A:T.36 GOL.24: 6 residues within 4Å: Chain A: E.256, Y.258, N.288, F.291, E.292, L.367 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.258, A:E.292 Water bridges: A:E.256

2 x ZN: ZINC ION(Non-covalent)

ZN.12: 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.13: 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

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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