Research workbench
Cryo-EM structure of DNMT5 in apo state
Analyse Cryo-EM structure of DNMT5 in apo state in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7R76
- Type
- protein
- Length
- 1,834 residues
- Chains
- 1
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA repair protein RAD8
- UniProt
- J9VI03
- Ligands
- ZN
- Pockets
- 20 · best druggability 0.88
Structure
electron microscopy · 1 distinct chain · 34% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA repair protein RAD8 | protein | 1834 | 34% helix, 15% strand | J9VI03 |
Ligands and binding sites
- ZN · Zinc ion · metal · 5 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1126 | 0.88 | 0.89 | 126 | empty |
| 2 | 791 | 0.80 | 0.83 | 84 | empty |
| 3 | 1059 | 0.72 | 0.76 | 104 | empty |
| 4 | 64 | 0.70 | 0.96 | 17 | empty |
| 5 | 66 | 0.70 | 0.96 | 22 | empty |
Compared structures
- 7R76 · Cryo-EM structure of DNMT5 in apo state · the same entry in another collection · chain A against A, TM-score 1.00
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 J9VI03
- Elsewhere: RCSB PDB 7R76 · PDBe 7R76 · UniProt J9VI03
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