Research workbench
T4DAM in complex with sinefungin and 16-mer oligonucleotide showing semi-specific and specific contact and flipped base
Analyse T4DAM in complex with sinefungin and 16-mer oligonucleotide showing… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1YFL
- Type
- protein + DNA
- Length
- 1,053 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-D(P*TP*CP*AP*CP*AP*GP*GP*AP*TP*CP*CP*TP*GP*TP*GP*A)-3'; DNA adenine methylase
- EC
- 2.1.1.72
- UniProt
- P04392
- Ligands
- SFG
- Pockets
- 15 · best druggability 0.77
Structure
x-ray diffraction · 4 distinct chains · 40% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| F, G, H, I | 5'-D(P*TP*CP*AP*CP*AP*GP*GP*AP*TP*CP*CP*TP*GP*TP*GP*A)-3' | dna | 16 | — | — |
| A, B | DNA adenine methylase (EC 2.1.1.72) | protein | 246 | 38% helix, 14% strand | P04392 |
| D | DNA adenine methylase (EC 2.1.1.72) | protein | 249 | 40% helix, 16% strand | P04392 |
| E | DNA adenine methylase (EC 2.1.1.72) | protein | 248 | 40% helix, 16% strand | P04392 |
Ligands and binding sites
- SFG · Sinefungin · ligand · 4 copies · chains G, A, B, I, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1197 | 0.77 | 0.80 | 70 | empty |
| 2 | 122 | 0.77 | 0.96 | 30 | SFG |
| 3 | 110 | 0.75 | 0.95 | 30 | SFG |
| 4 | 117 | 0.75 | 0.95 | 31 | SFG |
| 5 | 111 | 0.75 | 0.95 | 36 | SFG |
Interfaces
13 interfaces between chains.
- I–E · 761 Ų buried · 22 hydrogen bonds · protein-nucleic
- G–B · 755 Ų buried · 20 hydrogen bonds · protein-nucleic
- F–G · 689 Ų buried · 64 hydrogen bonds · nucleic-nucleic
- H–I · 687 Ų buried · 72 hydrogen bonds · nucleic-nucleic
- G–A · 604 Ų buried · 20 hydrogen bonds · protein-nucleic
Compared structures
- 1YFL · T4Dam in Complex with Sinefungin and 16-mer Oligonucleotide Showing Semi-specific and… · the same entry in another collection · chain F against F, 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 1YFL · PDBe 1YFL · UniProt P04392
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