MolNFT v1 · #28467 · protein + DNA
T4DAM in complex with adohcy and 13-mer oligonucleotide making non- and semi-specific (~1/4) contact
1YF3 · 5'-D(*AP*CP*CP*AP*TP*GP*AP*TP*CP*TP*GP*AP*C)-3': “T4DAM in complex with adohcy and 13-mer oligonucleotide making non- and semi-specific (~1/4) contact”. X-ray diffraction, 1 ligand (SAH), 6 pockets (best druggability 0.81). MolNFT…
- PDB
- 1YF3
- Type
- protein + DNA
- Length
- 534 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-D(*AP*CP*CP*AP*TP*GP*AP*TP*CP*TP*GP*AP*C)-3'…
- EC
- 2.1.1.72
- UniProt
- P04392
- Ligands
- SAH
- Pockets
- 6 · best druggability 0.81
Structure
x-ray diffraction · 4 distinct chains · 40% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | 5'-D(*AP*CP*CP*AP*TP*GP*AP*TP*CP*TP*GP*AP*C)-3' | dna | 13 | — | — |
| D | 5'-D(*TP*GP*TP*CP*AP*GP*AP*TP*CP*AP*TP*GP*G)-3' | dna | 13 | — | — |
| A | DNA adenine methylase (EC 2.1.1.72) | protein | 259 | 40% helix, 16% strand | P04392 |
| B | DNA adenine methylase (EC 2.1.1.72) | protein | 249 | 40% helix, 16% strand | P04392 |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · 2 copies · chains A, B
- GOL · Glycerol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 887 | 0.81 | 0.83 | 100 | SAH, GOL |
| 2 | 130 | 0.76 | 0.94 | 30 | SAH |
| 3 | 553 | 0.66 | 0.77 | 36 | empty |
| 4 | 81 | 0.47 | 0.82 | 15 | GOL |
| 5 | 65 | 0.38 | 0.79 | 12 | empty |
Interfaces
5 interfaces between chains.
- C–D · 516 Ų buried · 49 hydrogen bonds · nucleic-nucleic
- D–B · 271 Ų buried · 3 hydrogen bonds · protein-nucleic
- C–A · 266 Ų buried · 8 hydrogen bonds · protein-nucleic
- D–A · 263 Ų buried · 3 hydrogen bonds · protein-nucleic
- C–B · 215 Ų buried · 8 hydrogen bonds · protein-nucleic
Compared structures
- 1YF3 · T4Dam in Complex with AdoHcy and 13-mer Oligonucleotide Making Non- and Semi-specific… · 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 1YF3 · PDBe 1YF3 · UniProt P04392
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