SMTL ID : 3fde.2 (1 other biounit)

Mouse UHRF1 SRA domain bound with hemi-methylated CpG DNA, crystal structure in space group C222(1) at 1.4 A resolution

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.41 Å

Oligo State

monomer

Ligands

11 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.1: 2 residues within 4Å: Chain A: E.113, W.115 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.113 EDO.2: 5 residues within 4Å: Chain A: G.53, D.58, D.60, G.129, H.132 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.53, A:H.132 Water bridges: A:D.58, A:S.133 EDO.3: 5 residues within 4Å: Chain A: R.170, D.172, T.173, E.174, P.175 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.170, A:T.173 EDO.4: 3 residues within 4Å: Chain A: V.23 Chain B: C.8 Chain C: G.7 No protein-ligand interaction detected (PLIP) EDO.5: 4 residues within 4Å: Chain A: R.156, G.157, K.158, G.160 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.156, A:K.158 EDO.11: 7 residues within 4Å: Chain A: N.93 Chain B: A.3, T.4 Chain C: T.10, G.11 Ligands: EDO.15, NA.20 2 PLIP interactions: 2 interactions with chain A Water bridges: A:G.40, A:N.93 EDO.15: 7 residues within 4Å: Chain B: A.3, T.4 Chain C: T.10, G.11, G.12 Ligands: EDO.11, NA.20 No protein-ligand interaction detected (PLIP) EDO.16: 3 residues within 4Å: Chain C: G.11, G.12 Ligands: EDO.17 2 PLIP interactions: 2 interactions with chain A Water bridges: A:N.43, A:N.43 EDO.17: 3 residues within 4Å: Chain A: R.41 Chain C: G.11 Ligands: EDO.16 No protein-ligand interaction detected (PLIP) EDO.18: 4 residues within 4Å: Chain B: C.1 Chain C: T.10, G.11 Ligands: UNL.12 No protein-ligand interaction detected (PLIP) EDO.19: 5 residues within 4Å: Chain A: T.81 Chain B: C.8 Chain C: C.3, A.4, G.5 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.81 Water bridges: A:T.81, A:T.81

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

NA.6: 5 residues within 4Å: Chain A: P.33, H.34, V.35, A.36 Chain B: G.5 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.34, A:V.35, A:A.36 NA.20: 4 residues within 4Å: Chain C: T.10, G.11 Ligands: EDO.11, EDO.15 No protein-ligand interaction detected (PLIP)

7 x UNL: UNKNOWN LIGAND(Non-functional Binders)

UNL.7: 3 residues within 4Å: Chain A: N.63, Y.64, R.169 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.63 Salt bridges: A:R.169 UNL.8: 6 residues within 4Å: Chain A: L.99, N.100, C.101, H.102, Q.117, G.118 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.100, A:Q.117 UNL.9: 4 residues within 4Å: Chain A: D.60, S.133, K.134, Y.135 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:H.132, A:K.134 Water bridges: A:N.61, A:Y.135 UNL.10: 6 residues within 4Å: Chain A: G.71, G.72, R.73, S.86 Ligands: UNL.13, UNL.14 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:G.72, A:R.73, A:R.73, A:R.73, A:S.86 UNL.12: 2 residues within 4Å: Chain B: C.1 Ligands: EDO.18 No protein-ligand interaction detected (PLIP) UNL.13: 5 residues within 4Å: Chain A: G.71 Chain B: T.4, G.5 Ligands: UNL.10, UNL.14 3 PLIP interactions: 3 interactions with chain A Water bridges: A:G.72, A:T.91, A:N.92 UNL.14: 6 residues within 4Å: Chain A: R.73, L.75 Chain B: T.4, G.5 Ligands: UNL.10, UNL.13 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.73 Water bridges: A:G.71, A:R.73, A:L.75

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hashimoto, H. et al., UHRF1, a modular multi-domain protein, regulates replication-coupled crosstalk between DNA methylation and histone modifications. Epigenetics (2009)

Release Date

2009-01-06

Peptides

E3 ubiquitin-protein ligase UHRF1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

E3 ubiquitin-protein ligase UHRF1

Related Entries With Identical Sequence