SMTL ID : 4ayc.1

RNF8 RING domain structure

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-tetramer

Ligands

6 x SO4: SULFATE ION(Non-functional Binders)

SO4.1: 3 residues within 4Å: Chain A: S.118, S.119, E.120 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.119, A:S.119, A:E.120 SO4.2: 3 residues within 4Å: Chain A: K.95, D.96 Chain D: Y.102 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.96 SO4.3: 2 residues within 4Å: Chain A: L.7 Chain B: F.14 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:K.11 SO4.11: 3 residues within 4Å: Chain C: S.118, S.119, E.120 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:S.119, C:S.119, C:E.120 SO4.12: 3 residues within 4Å: Chain B: Y.102 Chain C: K.95, D.96 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:D.96 SO4.13: 2 residues within 4Å: Chain C: L.7 Chain D: F.14 1 PLIP interactions: 1 interactions with chain C Salt bridges: C:K.11

2 x CPQ: N,N-BIS(3-D-GLUCONAMIDOPROPYL)DEOXYCHOLAMIDE(Non-covalent)

CPQ.4: 7 residues within 4Å: Chain A: I.58, C.59, E.82, W.83, K.85, R.86, K.87 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:E.82, A:K.85 Hydrogen bonds: A:I.58, A:E.82, A:R.86, A:R.86 Water bridges: A:R.132 CPQ.14: 7 residues within 4Å: Chain C: I.58, C.59, E.82, W.83, K.85, R.86, K.87 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:E.82, C:K.85 Hydrogen bonds: C:I.58, C:E.82, C:R.86, C:R.86 Water bridges: C:R.132

8 x ZN: ZINC ION(Non-covalent)

ZN.5: 4 residues within 4Å: Chain A: C.71, H.73, C.90, C.93 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.71, A:H.73, A:C.90, A:C.93 ZN.6: 5 residues within 4Å: Chain A: C.56, C.59, C.76, C.79, R.132 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.56, A:C.59, A:C.76, A:C.79 ZN.7: 4 residues within 4Å: Chain B: C.71, H.73, C.90, C.93 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.71, B:H.73, B:C.90, B:C.93 ZN.8: 5 residues within 4Å: Chain B: C.56, C.59, C.76, C.79, R.132 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.56, B:C.59, B:C.76, B:C.79 ZN.15: 4 residues within 4Å: Chain C: C.71, H.73, C.90, C.93 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.71, C:H.73, C:C.90, C:C.93 ZN.16: 5 residues within 4Å: Chain C: C.56, C.59, C.76, C.79, R.132 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.56, C:C.59, C:C.76, C:C.79 ZN.17: 4 residues within 4Å: Chain D: C.71, H.73, C.90, C.93 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:C.71, D:H.73, D:C.90, D:C.93 ZN.18: 5 residues within 4Å: Chain D: C.56, C.59, C.76, C.79, R.132 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:C.56, D:C.59, D:C.76, D:C.79

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.9: 9 residues within 4Å: Chain B: M.84, I.97, K.98, K.100 Chain C: M.84, I.97, K.98, S.99, K.100 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:K.98, C:K.100, C:K.100 GOL.19: 9 residues within 4Å: Chain A: M.84, I.97, K.98, S.99, K.100 Chain D: M.84, I.97, K.98, K.100 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.98, A:K.100, A:K.100

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

CL.10: 1 residues within 4Å: Chain B: D.96 Ligand excluded by PLIP CL.20: 1 residues within 4Å: Chain D: D.96 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mattiroli, F. et al., Rnf168 Ubiquitinates K13-15 on H2A/H2Ax to Drive DNA Damage Signaling. Cell(Cambridge,Mass.) (2012)

Release Date

2012-09-26

Peptides

E3 UBIQUITIN-PROTEIN LIGASE RNF8: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

E3 UBIQUITIN-PROTEIN LIGASE RNF8