Research workbench
Structure of DNMT3A (R882H) in complex with cga DNA
Analyse Structure of DNMT3A (R882H) in complex with cga DNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6W89
- Type
- protein + DNA
- Length
- 1,989 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (cytosine-5)-methyltransferase 3A; DNA (cytosine-5)-methyltransferase 3-like; Cga DNA…
- EC
- 2.1.1.37
- UniProt
- Q9Y6K1, Q9UJW3
- Ligands
- SAH
- Pockets
- 20 · best druggability 0.77
Structure
x-ray diffraction · 8 distinct chains · 35% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D, J | DNA (cytosine-5)-methyltransferase 3A (EC 2.1.1.37) | protein | 285 | 33% helix, 18% strand | Q9Y6K1 |
| B | DNA (cytosine-5)-methyltransferase 3-like | protein | 194 | 37% helix, 16% strand | Q9UJW3 |
| C | DNA (cytosine-5)-methyltransferase 3-like | protein | 178 | 34% helix, 13% strand | Q9UJW3 |
| E | Cga DNA (25-mer) | dna | 24 | — | — |
| F, K, L | Cga DNA (25-mer) | dna | 25 | — | — |
| G | DNA (cytosine-5)-methyltransferase 3A (EC 2.1.1.37) | protein | 284 | 33% helix, 18% strand | Q9Y6K1 |
| H | DNA (cytosine-5)-methyltransferase 3-like | protein | 197 | 37% helix, 15% strand | Q9UJW3 |
| I | DNA (cytosine-5)-methyltransferase 3-like | protein | 182 | 36% helix, 15% strand | Q9UJW3 |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · 4 copies · chains A, D, G, J
- CIT · Citric acid · additive · 4 copies · chains A, D, G, J
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 18 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 370 | 0.77 | 0.87 | 59 | empty |
| 2 | 405 | 0.75 | 0.85 | 52 | empty |
| 3 | 1033 | 0.74 | 0.78 | 109 | empty |
| 4 | 448 | 0.69 | 0.81 | 52 | empty |
| 5 | 363 | 0.68 | 0.81 | 46 | SAH |
Interfaces
22 interfaces between chains.
- K–L · 1126 Ų buried · 97 hydrogen bonds · nucleic-nucleic
- E–F · 1102 Ų buried · 99 hydrogen bonds · nucleic-nucleic
- A–D · 1001 Ų buried · 14 hydrogen bonds · protein-protein
- G–J · 981 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 936 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (nucleotide modification).
Compared structures
- 6W89 · Structure of DNMT3A (R882H) in complex with CGA DNA · the same entry in another collection · chain K against K, 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 Q9Y6K1
- Every structure of UniProt Q9UJW3
- Elsewhere: RCSB PDB 6W89 · PDBe 6W89 · UniProt Q9Y6K1 · UniProt Q9UJW3
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