Research workbench
Crystal structure of the adenine-specific DNA methyltransferase M.TAQI complexed with the cofactor analog aeta and a 10 bp DNA containing 5- methylpyrimidin-2(1H)-one at the target base partner position
Analyse Crystal structure of the adenine-specific DNA methyltransferase M.TAQI… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2IH2
- Type
- protein + DNA
- Length
- 826 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-D(*GP*TP*TP*CP*GP*AP*TP*GP*TP*C)-3'; 5'-D(*GP*AP*CP*AP*(5PY)P*CP*GP*(6MA)P*AP*C)-3'…
- EC
- 2.1.1.72
- UniProt
- P14385
- Ligands
- NEA
- Pockets
- 8 · best druggability 0.55
Structure
x-ray diffraction · 3 distinct chains · 30% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, E | 5'-D(*GP*TP*TP*CP*GP*AP*TP*GP*TP*C)-3' | dna | 10 | — | — |
| C, F | 5'-D(*GP*AP*CP*AP*(5PY)P*CP*GP*(6MA)P*AP*C)-3' | dna | 10 | — | — |
| A, D | Modification methylase taqi (EC 2.1.1.72) | protein | 393 | 30% helix, 28% strand | P14385 |
Ligands and binding sites
- NEA · 5'-deoxy-5'-[2-(amino)ethylthio]adenosine · ligand · 2 copies · chains B, A, E, D
- GOL · Glycerol · additive · 5 copies · chains B, C, A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 200 | 0.55 | 0.78 | 31 | NEA, GOL |
| 2 | 198 | 0.53 | 0.78 | 33 | NEA, GOL |
| 3 | 195 | 0.53 | 0.78 | 31 | empty |
| 4 | 313 | 0.53 | 0.74 | 45 | empty |
| 5 | 192 | 0.48 | 0.76 | 25 | empty |
Interfaces
7 interfaces between chains.
- E–D · 1097 Ų buried · 17 hydrogen bonds · protein-nucleic
- B–A · 1093 Ų buried · 18 hydrogen bonds · protein-nucleic
- F–D · 990 Ų buried · 18 hydrogen bonds · protein-nucleic
- C–A · 972 Ų buried · 16 hydrogen bonds · protein-nucleic
- B–C · 499 Ų buried · 31 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 4 modified (nucleotide modification).
Compared structures
- 2IH2 · Crystal structure of the adenine-specific DNA methyltransferase M.TaqI complexed with the… · the same entry in another collection · chain E against E, TM-score 1.00
- P14385 · AlphaFold monomer V2.0 prediction for modification methylase taqi (P14385) · a predicted model of the same protein · chain A against A, TM-score 1.00
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 P14385
- Elsewhere: RCSB PDB 2IH2 · PDBe 2IH2 · UniProt P14385
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