MolNFT v1 · #39908 · protein + DNA
Engineered extrahelical base destabilization enhances sequence discrimination of DNA methyltransferase M.HHAI
2I9K · 5'-D(*T*GP*AP*TP*AP*GP*CP*GP*CP*TP*AP*TP*C)-3': “Engineered extrahelical base destabilization enhances sequence discrimination of DNA methyltransferase M.HHAI”. X-ray diffraction, 1 ligand (SAH), 5 pockets (best druggability 0.74).…
- PDB
- 2I9K
- Type
- protein + DNA
- Length
- 352 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-D(*T*GP*AP*TP*AP*GP*CP*GP*CP*TP*AP*TP*C)-3'; Modification methylase hhai
- EC
- 2.1.1.73
- UniProt
- P05102
- Ligands
- SAH
- Pockets
- 5 · best druggability 0.74
Structure
x-ray diffraction · 3 distinct chains · 33% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | 5'-D(*T*GP*AP*TP*AP*GP*CP*GP*CP*TP*AP*TP*C)-3' | dna | 12 | — | — |
| D | 5'-D(*T*GP*AP*TP*AP*GP*CP*GP*CP*TP*AP*TP*C)-3' | dna | 13 | — | — |
| A | Modification methylase hhai (EC 2.1.1.73) | protein | 327 | 33% helix, 19% 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
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 | 240 | 0.74 | 0.88 | 36 | SAH |
| 2 | 145 | 0.54 | 0.82 | 19 | empty |
| 3 | 95 | 0.38 | 0.76 | 13 | empty |
| 4 | 61 | 0.36 | 0.79 | 16 | empty |
| 5 | 52 | 0.27 | 0.75 | 11 | empty |
Interfaces
3 interfaces between chains.
- D–A · 967 Ų buried · 43 hydrogen bonds · protein-nucleic
- C–A · 722 Ų buried · 11 hydrogen bonds · protein-nucleic
- C–D · 544 Ų buried · 46 hydrogen bonds · nucleic-nucleic
Compared structures
- 2I9K · Engineered Extrahelical Base Destabilization Enhances Sequence Discrimination of DNA… · 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 0.99
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 2I9K · PDBe 2I9K · UniProt P05102
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