Research workbench
Crystal structure of bovine DNMT1 rfts domain in complex with H3K9ME3 and ubiquitin
Analyse Crystal structure of bovine DNMT1 rfts domain in complex with H3K9ME3 and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6PZV
- Type
- protein
- Length
- 811 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ubiquitin; DNA (cytosine-5)-methyltransferase 1; Histone H3.3
- EC
- 2.1.1.37
- UniProt
- J3QS39, Q24K09, P84243
- Ligands
- ZN
- Pockets
- 11 · best druggability 0.79
Structure
x-ray diffraction · 6 distinct chains · 26% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E | Ubiquitin | protein | 77 | 19% helix, 38% strand | J3QS39 |
| B, F | Ubiquitin | protein | 76 | 20% helix, 34% strand | J3QS39 |
| C | DNA (cytosine-5)-methyltransferase 1 (EC 2.1.1.37) | protein | 226 | 31% helix, 19% strand | Q24K09 |
| D | Histone H3.3 | protein | 18 | 0% helix, 33% strand | P84243 |
| G | DNA (cytosine-5)-methyltransferase 1 (EC 2.1.1.37) | protein | 242 | 30% helix, 18% strand | Q24K09 |
| H | Histone H3.3 | protein | 19 | 0% helix, 32% strand | P84243 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1058 | 0.79 | 0.81 | 91 | empty |
| 2 | 286 | 0.71 | 0.85 | 53 | empty |
| 3 | 182 | 0.66 | 0.85 | 25 | empty |
| 4 | 172 | 0.64 | 0.85 | 32 | empty |
| 5 | 152 | 0.64 | 0.85 | 21 | empty |
Interfaces
15 interfaces between chains.
- E–G · 1072 Ų buried · 9 hydrogen bonds · protein-protein
- F–G · 953 Ų buried · 6 hydrogen bonds · protein-protein
- G–H · 950 Ų buried · 22 hydrogen bonds · protein-protein
- A–C · 881 Ų buried · 7 hydrogen bonds · protein-protein
- C–D · 858 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide, 2 modified (disulfide, methylation).
Compared structures
- 6PZV · Crystal Structure of Bovine DNMT1 RFTS domain in complex with H3K9me3 and Ubiquitin · the same entry in another collection · chain H against H, TM-score 1.00
- Q24K09 · AlphaFold monomer V2.0 prediction for DNA (cytosine-5)-methyltransferase 1 (Q24K09) · a predicted model of the same protein · chain C against A, TM-score 0.80
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt J3QS39
- Every structure of UniProt Q24K09
- Every structure of UniProt P84243
- Elsewhere: RCSB PDB 6PZV · PDBe 6PZV · UniProt J3QS39 · UniProt Q24K09 · UniProt P84243
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