Research workbench
Ternary structure of T4DAM with adohcy and DNA
Analyse Ternary structure of T4DAM with adohcy and DNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1Q0T
- Type
- protein + DNA
- Length
- 506 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-D(*AP*CP*AP*GP*GP*AP*TP*CP*CP*TP*GP*T)-3'; DNA adenine methylase
- EC
- 2.1.1.72
- UniProt
- P04392
- Ligands
- SAH, IOD
- Pockets
- 3 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C, D | 5'-D(*AP*CP*AP*GP*GP*AP*TP*CP*CP*TP*GP*T)-3' | dna | 12 | — | — |
| A, B | DNA adenine methylase (EC 2.1.1.72) | protein | 241 | 39% helix, 14% strand | P04392 |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · 2 copies · chains A, B
- IOD · Iodide ion · ion · 2 copies · chains C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 926 | 0.73 | 0.78 | 73 | SAH |
| 2 | 156 | 0.69 | 0.89 | 36 | SAH |
| 3 | 518 | 0.63 | 0.76 | 43 | IOD |
Interfaces
5 interfaces between chains.
- C–D · 529 Ų buried · 52 hydrogen bonds · nucleic-nucleic
- C–A · 245 Ų buried · 7 hydrogen bonds · protein-nucleic
- C–B · 242 Ų buried · 5 hydrogen bonds · protein-nucleic
- D–A · 115 Ų buried · 2 hydrogen bonds · protein-nucleic
- D–B · 48 Ų buried · 0 hydrogen bonds · protein-nucleic
Compared structures
- 1Q0T · Ternary Structure of T4DAM with AdoHcy and DNA · the same entry in another collection · chain B against B, 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 P04392
- Elsewhere: RCSB PDB 1Q0T · PDBe 1Q0T · UniProt P04392
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