MolNFT v1 · #160975 · protein
Crystal structure of bovine DNMT1 rfts domain in complex with H3K9ME3 and ubiquitin
6PZV: “Crystal structure of bovine DNMT1 rfts domain in complex with H3K9ME3 and ubiquitin”. X-ray diffraction, 1 ligand (ZN), 11 pockets (best druggability 0.79). MolNFT v1 #160975 on GenesisL1: 3D structure, binding sites and pockets in…
- 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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