Research workbench
Structure of ternary complex of hhai methyltransferase mutant (T250G) in complex with DNA and adohcy
Analyse Structure of ternary complex of hhai methyltransferase mutant (T250G) in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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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