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Cryo-EM structure of DNMT5 quaternary complex with hemimethylated DNA, AMP-pnp and sah
Analyse Cryo-EM structure of DNMT5 quaternary complex with hemimethylated DNA, AMP-pnp… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7R78
- Type
- protein + DNA
- Length
- 1,898 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA repair protein RAD8; DNA (5'-D(P*CP*AP*GP*(5CM)P*GP*CP*AP*T)-3'); DNA…
- UniProt
- J9VI03
- Ligands
- SAH, ANP, ZN, MG
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · 3 distinct chains · 33% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA repair protein RAD8 | protein | 1880 | 33% helix, 14% strand | J9VI03 |
| D | DNA (5'-D(P*CP*AP*GP*(5CM)P*GP*CP*AP*T)-3') | dna | 8 | — | — |
| E | DNA (5'-D(*TP*GP*CP*GP*CP*TP*GP*AP*CP*A)-3') | dna | 10 | — | — |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · chains A, E
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · chains A
- ZN · Zinc ion · metal · 5 copies · chains A
- MG · Magnesium ion · metal · 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, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1160 | 0.86 | 0.88 | 129 | empty |
| 2 | 1144 | 0.81 | 0.82 | 82 | empty |
| 3 | 1012 | 0.80 | 0.82 | 83 | SAH |
| 4 | 760 | 0.76 | 0.81 | 86 | empty |
| 5 | 81 | 0.75 | 0.97 | 20 | empty |
Interfaces
3 interfaces between chains.
- A–E · 909 Ų buried · 15 hydrogen bonds · protein-nucleic
- A–D · 784 Ų buried · 16 hydrogen bonds · protein-nucleic
- D–E · 316 Ų buried · 21 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 7R78 · cryo-EM structure of DNMT5 quaternary complex with hemimethylated DNA, AMP-PNP and SAH · 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 7R78 · PDBe 7R78 · UniProt J9VI03
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