Research workbench
Ternary structure of hhai methyltransferase with hemimethylated DNA and adohcy
Analyse Ternary structure of hhai methyltransferase with hemimethylated DNA and adohcy in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5MHT
- Type
- protein + DNA
- Length
- 351 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (5'-D(*CP*CP*AP*TP*GP*(5CM) P*GP*CP*TP*GP*AP*C)-3'); DNA…
- EC
- 2.1.1.7
- UniProt
- P05102
- Ligands
- SAH
- Pockets
- 6 · best druggability 0.74
Structure
x-ray diffraction · 3 distinct chains · 30% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | DNA (5'-D(*CP*CP*AP*TP*GP*(5CM) P*GP*CP*TP*GP*AP*C)-3') | dna | 12 | — | — |
| D | DNA (5'-D(*GP*TP*CP*AP*GP*CP*GP*CP*AP*TP*GP*G)- 3') | dna | 12 | — | — |
| A | Protein (hhai methyltransferase) (EC 2.1.1.7) | protein | 327 | 30% helix, 18% strand | P05102 |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · chains D, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 345 | 0.74 | 0.86 | 40 | SAH |
| 2 | 72 | 0.74 | 0.99 | 22 | empty |
| 3 | 186 | 0.57 | 0.81 | 22 | empty |
| 4 | 212 | 0.56 | 0.79 | 25 | empty |
| 5 | 75 | 0.35 | 0.77 | 13 | empty |
Interfaces
3 interfaces between chains.
- D–A · 1017 Ų buried · 27 hydrogen bonds · protein-nucleic
- C–A · 714 Ų buried · 11 hydrogen bonds · protein-nucleic
- C–D · 556 Ų buried · 35 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 5MHT · Ternary structure of hhai methyltransferase with hemimethylated DNA and adohcy · the same entry in another collection · chain A against A, 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 0.98
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 5MHT · PDBe 5MHT · UniProt P05102
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