MolNFT v1 · #120922 · protein
Crystal structure of M1.HPYAVI-SAM complex
5HFJ · Adenine specific DNA methyltransferase (dpna): “Crystal structure of M1.HPYAVI-SAM complex”. X-ray diffraction, 1 ligand (SAM), 20 pockets (best druggability 0.71). MolNFT v1 #120922 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5HFJ
- Type
- protein
- Length
- 1,567 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Adenine specific DNA methyltransferase (dpna)
- UniProt
- O24891
- Ligands
- SAM
- Pockets
- 20 · best druggability 0.71
Structure
x-ray diffraction · 8 distinct chains · 30% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Adenine specific DNA methyltransferase (dpna) | protein | 201 | 29% helix, 26% strand | O24891 |
| B | Adenine specific DNA methyltransferase (dpna) | protein | 194 | 29% helix, 26% strand | O24891 |
| C | Adenine specific DNA methyltransferase (dpna) | protein | 204 | 30% helix, 25% strand | O24891 |
| D | Adenine specific DNA methyltransferase (dpna) | protein | 188 | 32% helix, 27% strand | O24891 |
| E | Adenine specific DNA methyltransferase (dpna) | protein | 193 | 31% helix, 26% strand | O24891 |
| F | Adenine specific DNA methyltransferase (dpna) | protein | 194 | 31% helix, 26% strand | O24891 |
| G | Adenine specific DNA methyltransferase (dpna) | protein | 200 | 28% helix, 25% strand | O24891 |
| H | Adenine specific DNA methyltransferase (dpna) | protein | 193 | 31% helix, 27% strand | O24891 |
Ligands and binding sites
- SAM · S-adenosylmethionine · ligand · 8 copies · chains A, B, C, D, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 732 | 0.71 | 0.77 | 65 | empty |
| 2 | 633 | 0.65 | 0.75 | 62 | empty |
| 3 | 329 | 0.63 | 0.79 | 55 | SAM |
| 4 | 299 | 0.59 | 0.78 | 49 | SAM |
| 5 | 153 | 0.57 | 0.82 | 32 | SAM |
Interfaces
10 interfaces between chains.
- A–B · 2102 Ų buried · 40 hydrogen bonds · protein-protein
- F–G · 2078 Ų buried · 40 hydrogen bonds · protein-protein
- C–E · 2012 Ų buried · 34 hydrogen bonds · protein-protein
- D–H · 1985 Ų buried · 37 hydrogen bonds · protein-protein
- F–H · 201 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 5HFJ · crystal structure of M1.HpyAVI-SAM complex · 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 O24891
- Elsewhere: RCSB PDB 5HFJ · PDBe 5HFJ · UniProt O24891
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.