MolNFT v1 · #120891 · protein
Crystal structure of M1.HPYAVI
5HEK · Adenine specific DNA methyltransferase (dpna): “Crystal structure of M1.HPYAVI”. X-ray diffraction, 10 pockets (best druggability 0.48). MolNFT v1 #120891 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5HEK
- Type
- protein
- Length
- 744 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Adenine specific DNA methyltransferase (dpna)
- UniProt
- O24891
- Pockets
- 10 · best druggability 0.48
Structure
x-ray diffraction · 4 distinct chains · 31% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Adenine specific DNA methyltransferase (dpna) | protein | 197 | 28% helix, 25% strand | O24891 |
| B | Adenine specific DNA methyltransferase (dpna) | protein | 185 | 33% helix, 26% strand | O24891 |
| C | Adenine specific DNA methyltransferase (dpna) | protein | 185 | 31% helix, 26% strand | O24891 |
| D | Adenine specific DNA methyltransferase (dpna) | protein | 177 | 31% helix, 27% strand | O24891 |
Pockets
10 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 190 | 0.48 | 0.75 | 31 | empty |
| 2 | 137 | 0.46 | 0.77 | 30 | empty |
| 3 | 127 | 0.45 | 0.77 | 15 | empty |
| 4 | 133 | 0.45 | 0.77 | 27 | empty |
| 5 | 64 | 0.44 | 0.82 | 14 | empty |
Interfaces
5 interfaces between chains.
- A–C · 2165 Ų buried · 35 hydrogen bonds · protein-protein
- B–D · 1947 Ų buried · 42 hydrogen bonds · protein-protein
- A–B · 673 Ų buried · 5 hydrogen bonds · protein-protein
- A–D · 21 Ų buried · 0 hydrogen bonds · protein-protein
- C–D · 17 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5HEK · crystal structure of M1.HpyAVI · 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 5HEK · PDBe 5HEK · UniProt O24891
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