MolNFT v1 · #156874 · protein + DNA
Ternary structure of hhai methyltransferase with adohcy and DNA containing 4'-thio-2'DEOXYCYTIDINE at the target
6MHT · DNA (5'-D(P*CP*CP*AP*TP*GP*(5CM)P*GP*CP*TP*GP*AP*C)-3'): “Ternary structure of hhai methyltransferase with adohcy and DNA containing 4'-thio-2'DEOXYCYTIDINE at the…”. X-ray diffraction, 1 ligand (SAM), 6 pockets (best druggability…
- PDB
- 6MHT
- Type
- protein + DNA
- Length
- 351 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (5'-D(P*CP*CP*AP*TP*GP*(5CM)P*GP*CP*TP*GP*AP*C)-3'); DNA…
- EC
- 2.1.1.73
- UniProt
- P05102
- Ligands
- SAM
- Pockets
- 6 · best druggability 0.74
Structure
x-ray diffraction · 3 distinct chains · 32% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | DNA (5'-D(P*CP*CP*AP*TP*GP*(5CM)P*GP*CP*TP*GP*AP*C)-3') | dna | 12 | — | — |
| D | DNA (5'-D(P*GP*TP*CP*AP*GP*(4SC)P*GP*CP*AP*TP*GP*G)-3') | dna | 12 | — | — |
| A | Cytosine-specific methyltransferase hhai (EC 2.1.1.73) | protein | 327 | 32% helix, 18% strand | P05102 |
Ligands and binding sites
- SAM · S-adenosylmethionine · 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 | 67 | 0.74 | 0.99 | 23 | empty |
| 2 | 326 | 0.73 | 0.85 | 39 | SAM |
| 3 | 186 | 0.59 | 0.82 | 19 | empty |
| 4 | 225 | 0.57 | 0.79 | 26 | empty |
| 5 | 86 | 0.36 | 0.76 | 13 | empty |
Interfaces
3 interfaces between chains.
- D–A · 1027 Ų buried · 25 hydrogen bonds · protein-nucleic
- C–A · 698 Ų buried · 10 hydrogen bonds · protein-nucleic
- C–D · 553 Ų buried · 44 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 2 modified, 1 covalent (nucleotide modification, covalent ligand).
Compared structures
- 6MHT · Ternary structure of hhai methyltransferase with adohcy and DNA containing… · the same entry in another collection · chain C against C, 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 6MHT · PDBe 6MHT · UniProt P05102
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