MolNFT v1 · #6675 · protein + DNA
Structure of ternary complex of hhai methyltransferase mutant (T250G) in complex with DNA and adohcy
1FJX · DNA (5'-D(*TP*GP*AP*TP*AP*GP*CP*GP*CP*TP*AP*TP*C)-3'): “Structure of ternary complex of hhai methyltransferase mutant (T250G) in complex with DNA and adohcy”. X-ray diffraction, 2 ligands (SAH, SO4), 5 pockets (best druggability…
- PDB
- 1FJX
- Type
- protein + DNA
- Length
- 353 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (5'-D(*TP*GP*AP*TP*AP*GP*CP*GP*CP*TP*AP*TP*C)-3'); Hhai DNA methyltransferase
- EC
- 2.1.1.73
- UniProt
- P05102
- Ligands
- SAH, SO4
- Pockets
- 5 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 34% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C, D | DNA (5'-D(*TP*GP*AP*TP*AP*GP*CP*GP*CP*TP*AP*TP*C)-3') | dna | 13 | — | — |
| A | Hhai DNA methyltransferase (EC 2.1.1.73) | protein | 327 | 34% helix, 19% strand | P05102 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 239 | 0.74 | 0.88 | 36 | SAH |
| 2 | 186 | 0.66 | 0.86 | 40 | empty |
| 3 | 124 | 0.44 | 0.77 | 16 | empty |
| 4 | 63 | 0.42 | 0.82 | 18 | empty |
| 5 | 58 | 0.30 | 0.76 | 11 | empty |
Interfaces
3 interfaces between chains.
- D–A · 1004 Ų buried · 31 hydrogen bonds · protein-nucleic
- C–A · 842 Ų buried · 13 hydrogen bonds · protein-nucleic
- C–D · 539 Ų buried · 39 hydrogen bonds · nucleic-nucleic
Compared structures
- 1FJX · Structure of ternary complex of hhai methyltransferase mutant (T250G) in complex with DNA… · the same entry in another collection · chain D against D, TM-score 1.00
- P05102 · AlphaFold monomer V2.0 prediction for modification methylase hhai (P05102) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 P05102
- Elsewhere: RCSB PDB 1FJX · PDBe 1FJX · UniProt P05102
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