Research workbench
Crystal structure of the adenine-specific DNA methyltransferase M.TAQI complexed with the cofactor analog aeta and a 10 bp DNA containing 2- aminopurine at the target position and an abasic site analog 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
- 2IBT
- 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*(2PR)P*TP*GP*TP*C)-3'; 5'-D(*GP*AP*CP*AP*(3DR)P*CP*GP*(6MA)P*AP*C)-3'…
- EC
- 2.1.1.72
- UniProt
- P14385
- Ligands
- NEA
- Pockets
- 9 · best druggability 0.63
Structure
x-ray diffraction · 3 distinct chains · 29% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, E | 5'-D(*GP*TP*TP*CP*GP*(2PR)P*TP*GP*TP*C)-3' | dna | 10 | — | — |
| C, F | 5'-D(*GP*AP*CP*AP*(3DR)P*CP*GP*(6MA)P*AP*C)-3' | dna | 10 | — | — |
| A, D | Modification methylase taqi (EC 2.1.1.72) | protein | 393 | 29% 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 · 7 copies · chains A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 287 | 0.63 | 0.80 | 37 | empty |
| 2 | 472 | 0.60 | 0.75 | 51 | empty |
| 3 | 208 | 0.54 | 0.79 | 30 | empty |
| 4 | 182 | 0.54 | 0.79 | 30 | NEA, GOL |
| 5 | 195 | 0.54 | 0.78 | 30 | NEA, GOL |
Interfaces
7 interfaces between chains.
- B–A · 1093 Ų buried · 16 hydrogen bonds · protein-nucleic
- E–D · 1036 Ų buried · 18 hydrogen bonds · protein-nucleic
- F–D · 956 Ų buried · 15 hydrogen bonds · protein-nucleic
- C–A · 923 Ų buried · 14 hydrogen bonds · protein-nucleic
- E–F · 448 Ų buried · 31 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 6 modified (nucleotide modification).
Compared structures
- 2IBT · 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 2IBT · PDBe 2IBT · UniProt P14385
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