Research workbench
Structure of the replication foci-targeting sequence of human DNA cytosine methyltransferase DNMT1
Analyse Structure of the replication foci-targeting sequence of human DNA cytosine… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3EPZ
- Type
- protein
- Length
- 450 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (cytosine-5)-methyltransferase 1
- EC
- 2.1.1.37
- UniProt
- P26358
- Ligands
- BGC, ZN, NA
- Pockets
- 4 · best druggability 0.61
Structure
x-ray diffraction · 2 distinct chains · 34% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA (cytosine-5)-methyltransferase 1 (EC 2.1.1.37) | protein | 227 | 37% helix, 20% strand | P26358 |
| B | DNA (cytosine-5)-methyltransferase 1 (EC 2.1.1.37) | protein | 223 | 31% helix, 17% strand | P26358 |
Ligands and binding sites
- BGC · beta-D-glucopyranose · sugar · chains A
- ZN · Zinc ion · metal · 2 copies · chains A, B
- NA · Sodium ion · metal · chains A
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 400 | 0.61 | 0.76 | 50 | BGC |
| 2 | 138 | 0.53 | 0.81 | 26 | empty |
| 3 | 74 | 0.36 | 0.77 | 14 | empty |
| 4 | 56 | 0.26 | 0.73 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 637 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 modified (engineered).
Compared structures
- 3EPZ · Structure of the replication foci-targeting sequence of human DNA cytosine… · the same entry in another collection · chain A against A, TM-score 1.00
- P26358 · AlphaFold monomer V2.0 prediction for DNA (cytosine-5)-methyltransferase 1 (P26358) · a predicted model of the same protein · chain B against A, TM-score 0.68
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 P26358
- Elsewhere: RCSB PDB 3EPZ · PDBe 3EPZ · UniProt P26358
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